├── .github
    └── ISSUE_TEMPLATE
    │   ├── bug-or-error-report.md
    │   └── question-or-feature-request-.md
├── .gitignore
├── .readthedocs.yaml
├── LICENSE
├── Makefile
├── README.md
├── VERSION
├── doc
    ├── FAQ.rst
    ├── OPTION.rst
    ├── QSTART.rst
    ├── TEST1.rst
    ├── TEST2.pdf
    ├── TEST2.rst
    ├── TEST3.pdf
    ├── TEST3.rst
    ├── TEST4.pdf
    ├── TEST4.rst
    ├── TEST5.rst
    ├── UTILITY.rst
    ├── conf.py
    ├── index.rst
    ├── requirements.txt
    └── run.cfg
├── lib
    ├── Makefile
    ├── align.c
    ├── align.h
    ├── bseq.c
    ├── bseq.h
    ├── bsort.c
    ├── bsort.h
    ├── config_parser.py
    ├── ctg_cns.c
    ├── ctg_cns.h
    ├── ctg_cns.py
    ├── dag.c
    ├── htslib
    │   ├── INSTALL
    │   ├── LICENSE
    │   ├── Makefile
    │   ├── NEWS
    │   ├── README
    │   ├── bcf_sr_sort.c
    │   ├── bcf_sr_sort.h
    │   ├── bgzf.c
    │   ├── bgzip.1
    │   ├── bgzip.c
    │   ├── config.h.in
    │   ├── config.mk.in
    │   ├── configure
    │   ├── configure.ac
    │   ├── cram
    │   │   ├── cram.h
    │   │   ├── cram_codecs.c
    │   │   ├── cram_codecs.h
    │   │   ├── cram_decode.c
    │   │   ├── cram_decode.h
    │   │   ├── cram_encode.c
    │   │   ├── cram_encode.h
    │   │   ├── cram_external.c
    │   │   ├── cram_index.c
    │   │   ├── cram_index.h
    │   │   ├── cram_io.c
    │   │   ├── cram_io.h
    │   │   ├── cram_samtools.c
    │   │   ├── cram_samtools.h
    │   │   ├── cram_stats.c
    │   │   ├── cram_stats.h
    │   │   ├── cram_structs.h
    │   │   ├── files.c
    │   │   ├── mFILE.c
    │   │   ├── mFILE.h
    │   │   ├── misc.h
    │   │   ├── open_trace_file.c
    │   │   ├── open_trace_file.h
    │   │   ├── os.h
    │   │   ├── pooled_alloc.c
    │   │   ├── pooled_alloc.h
    │   │   ├── rANS_byte.h
    │   │   ├── rANS_static.c
    │   │   ├── rANS_static.h
    │   │   ├── sam_header.c
    │   │   ├── sam_header.h
    │   │   ├── string_alloc.c
    │   │   └── string_alloc.h
    │   ├── errmod.c
    │   ├── faidx.5
    │   ├── faidx.c
    │   ├── hfile.c
    │   ├── hfile_gcs.c
    │   ├── hfile_internal.h
    │   ├── hfile_libcurl.c
    │   ├── hfile_net.c
    │   ├── hfile_s3.c
    │   ├── hts.c
    │   ├── hts_internal.h
    │   ├── hts_os.c
    │   ├── htsfile.1
    │   ├── htsfile.c
    │   ├── htslib.mk
    │   ├── htslib.pc.in
    │   ├── htslib
    │   │   ├── bgzf.h
    │   │   ├── cram.h
    │   │   ├── faidx.h
    │   │   ├── hfile.h
    │   │   ├── hts.h
    │   │   ├── hts_defs.h
    │   │   ├── hts_endian.h
    │   │   ├── hts_log.h
    │   │   ├── hts_os.h
    │   │   ├── kbitset.h
    │   │   ├── kfunc.h
    │   │   ├── khash.h
    │   │   ├── khash_str2int.h
    │   │   ├── klist.h
    │   │   ├── knetfile.h
    │   │   ├── kseq.h
    │   │   ├── ksort.h
    │   │   ├── kstring.h
    │   │   ├── regidx.h
    │   │   ├── sam.h
    │   │   ├── synced_bcf_reader.h
    │   │   ├── tbx.h
    │   │   ├── thread_pool.h
    │   │   ├── vcf.h
    │   │   ├── vcf_sweep.h
    │   │   └── vcfutils.h
    │   ├── htslib_vars.mk
    │   ├── kfunc.c
    │   ├── knetfile.c
    │   ├── kstring.c
    │   ├── m4
    │   │   └── hts_prog_cc_warnings.m4
    │   ├── md5.c
    │   ├── multipart.c
    │   ├── os
    │   │   ├── lzma_stub.h
    │   │   └── rand.c
    │   ├── plugin.c
    │   ├── probaln.c
    │   ├── realn.c
    │   ├── regidx.c
    │   ├── sam.5
    │   ├── sam.c
    │   ├── synced_bcf_reader.c
    │   ├── tabix.1
    │   ├── tabix.c
    │   ├── tbx.c
    │   ├── test
    │   │   ├── auxf#values.sam
    │   │   ├── auxf#values_java.cram
    │   │   ├── auxf.fa
    │   │   ├── auxf.fa.fai
    │   │   ├── bgziptest.txt
    │   │   ├── bgziptest.txt.gz
    │   │   ├── bgziptest.txt.gz.gzi
    │   │   ├── c1#bounds.sam
    │   │   ├── c1#clip.sam
    │   │   ├── c1#noseq.sam
    │   │   ├── c1#pad1.sam
    │   │   ├── c1#pad2.sam
    │   │   ├── c1#pad3.sam
    │   │   ├── c1#unknown.sam
    │   │   ├── c1.fa
    │   │   ├── c1.fa.fai
    │   │   ├── c2#pad.sam
    │   │   ├── c2.fa
    │   │   ├── c2.fa.fai
    │   │   ├── ce#1.sam
    │   │   ├── ce#1000.sam
    │   │   ├── ce#2.sam
    │   │   ├── ce#5.sam
    │   │   ├── ce#5b.sam
    │   │   ├── ce#5b_java.cram
    │   │   ├── ce#large_seq.sam
    │   │   ├── ce#supp.sam
    │   │   ├── ce#tag_depadded.sam
    │   │   ├── ce#tag_padded.sam
    │   │   ├── ce#unmap.sam
    │   │   ├── ce#unmap1.sam
    │   │   ├── ce#unmap2.sam
    │   │   ├── ce.fa
    │   │   ├── ce.fa.fai
    │   │   ├── compare_sam.pl
    │   │   ├── cross_validate.sh
    │   │   ├── faidx.fa
    │   │   ├── fastqs.fq
    │   │   ├── fastqs_README.txt
    │   │   ├── fieldarith.c
    │   │   ├── fieldarith.sam
    │   │   ├── formatcols.vcf
    │   │   ├── formatmissing-out.vcf
    │   │   ├── formatmissing.vcf
    │   │   ├── hfile.c
    │   │   ├── hts_endian.c
    │   │   ├── md#1.sam
    │   │   ├── md.fa
    │   │   ├── md.fa.fai
    │   │   ├── noroundtrip-out.vcf
    │   │   ├── noroundtrip.vcf
    │   │   ├── range.bam
    │   │   ├── range.bam.bai
    │   │   ├── range.cram
    │   │   ├── range.cram.crai
    │   │   ├── realn01.fa
    │   │   ├── realn01.fa.fai
    │   │   ├── realn01.sam
    │   │   ├── realn01_exp-a.sam
    │   │   ├── realn01_exp-e.sam
    │   │   ├── realn01_exp.sam
    │   │   ├── realn02-r.sam
    │   │   ├── realn02.fa
    │   │   ├── realn02.fa.fai
    │   │   ├── realn02.sam
    │   │   ├── realn02_exp-a.sam
    │   │   ├── realn02_exp-e.sam
    │   │   ├── realn02_exp.sam
    │   │   ├── sam.c
    │   │   ├── tabix
    │   │   │   ├── bed_file.bed
    │   │   │   ├── gff_file.gff
    │   │   │   ├── large_chr.vcf
    │   │   │   ├── tabix.tst
    │   │   │   ├── test-tabix.sh
    │   │   │   └── vcf_file.vcf
    │   │   ├── test-bcf-sr.c
    │   │   ├── test-bcf-sr.pl
    │   │   ├── test-bcf-translate.c
    │   │   ├── test-logging.pl
    │   │   ├── test-regidx.c
    │   │   ├── test-vcf-api.c
    │   │   ├── test-vcf-hdr-in.vcf
    │   │   ├── test-vcf-sweep.c
    │   │   ├── test.pl
    │   │   ├── test_bgzf.c
    │   │   ├── test_realn.c
    │   │   ├── test_view.c
    │   │   ├── thrash_threads1.c
    │   │   ├── thrash_threads2.c
    │   │   ├── thrash_threads3.c
    │   │   ├── thrash_threads4.c
    │   │   ├── thrash_threads5.c
    │   │   ├── thrash_threads6.c
    │   │   ├── thread_pool.md
    │   │   ├── xx#blank.sam
    │   │   ├── xx#large_aux.sam
    │   │   ├── xx#large_aux2.sam
    │   │   ├── xx#large_aux_java.cram
    │   │   ├── xx#minimal.sam
    │   │   ├── xx#pair.sam
    │   │   ├── xx#repeated.sam
    │   │   ├── xx#rg.sam
    │   │   ├── xx#tlen.sam
    │   │   ├── xx#tlen2.sam
    │   │   ├── xx#triplet.sam
    │   │   ├── xx#unsorted.sam
    │   │   ├── xx.fa
    │   │   └── xx.fa.fai
    │   ├── textutils.c
    │   ├── textutils_internal.h
    │   ├── thread_pool.c
    │   ├── thread_pool_internal.h
    │   ├── vcf.5
    │   ├── vcf.c
    │   ├── vcf_sweep.c
    │   ├── vcfutils.c
    │   └── version.sh
    ├── index.c
    ├── index.h
    ├── kit.c
    ├── kit.py
    ├── mseq.h
    ├── nextcorrect.c
    ├── nextcorrect.h
    ├── nextcorrect.py
    ├── ovl.c
    ├── ovl.h
    ├── ovlseq.c
    └── split_cns.py
├── minimap2
    ├── LICENSE.txt
    ├── MANIFEST.in
    ├── Makefile
    ├── NEWS.md
    ├── README.md
    ├── align.c
    ├── bseq.c
    ├── bseq.h
    ├── chain.c
    ├── cookbook.md
    ├── esterr.c
    ├── example.c
    ├── format.c
    ├── hit.c
    ├── index.c
    ├── kalloc.c
    ├── kalloc.h
    ├── kdq.h
    ├── ketopt.h
    ├── khash.h
    ├── kseq.h
    ├── ksort.h
    ├── ksw2.h
    ├── ksw2_dispatch.c
    ├── ksw2_extd2_sse.c
    ├── ksw2_exts2_sse.c
    ├── ksw2_extz2_sse.c
    ├── ksw2_ll_sse.c
    ├── kthread.c
    ├── kthread.h
    ├── kvec.h
    ├── main.c
    ├── map.c
    ├── minimap.h
    ├── minimap2.1
    ├── misc.c
    ├── misc
    │   ├── README.md
    │   └── paftools.js
    ├── mmpriv.h
    ├── options.c
    ├── pe.c
    ├── python
    │   ├── README.rst
    │   ├── cmappy.h
    │   ├── cmappy.pxd
    │   ├── mappy.pyx
    │   └── minimap2.py
    ├── sdust.c
    ├── sdust.h
    ├── setup.py
    ├── sketch.c
    ├── splitidx.c
    ├── sse2neon
    │   └── emmintrin.h
    └── test
    │   ├── MT-human.fa
    │   ├── MT-orang.fa
    │   ├── q-inv.fa
    │   ├── q2.fa
    │   ├── t-inv.fa
    │   └── t2.fa
├── nextDenovo
├── test_data
    ├── input.fofn
    ├── reads_test.fa.gz
    └── run.cfg
└── util
    ├── Makefile
    ├── bam_sort.c
    ├── khash.h
    ├── kseq.h
    ├── ng
        ├── Makefile
        ├── asg.c
        ├── asg.h
        ├── common.h
        ├── ctg.c
        ├── ctg.h
        ├── edge.c
        ├── edge.h
        ├── kit.c
        ├── kit.h
        ├── main.c
        ├── node.c
        ├── node.h
        ├── opt.c
        ├── opt.h
        ├── out.c
        └── out.h
    ├── ovl_cvt.c
    ├── ovl_sort.c
    ├── ovl_sort.h
    ├── seq_bit.c
    ├── seq_dump.c
    ├── seq_stat.c
    ├── thpool.c
    └── thpool.h


/.github/ISSUE_TEMPLATE/bug-or-error-report.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | name: Bug or Error report
 3 | about: Create a report to help us improve
 4 | title: ''
 5 | labels: ''
 6 | assignees: ''
 7 | 
 8 | ---
 9 | 
10 | **Describe the bug**
11 | A clear and concise description of what the bug or error is.
12 | 
13 | **Error message**
14 | Paste the complete log message, include the main task log and failed subtask log.
15 | The main task log is usually located  in your working directory and is named `pidXXX.log.info` and the main task log will tell you the failed subtask log in the last few lines, such as:
16 | <pre>
17 | [ERROR] 2020-07-01 11:06:57,184 cns_align failed: please check the following logs:
18 | [ERROR] 2020-07-01 11:06:57,185 <ins>~/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align0/nextDenovo.sh.e</ins>
19 | </pre>
20 | 
21 | **Genome characteristics**
22 | `genome size, heterozygous rate, repeat content...`
23 | 
24 | **Input data**
25 | `Total base count, sequencing depth, average/N50 read length...`
26 | 
27 | **Config file**
28 | Please paste the complete content of the Config file (`run.cfg`) to here.
29 | 
30 | **Operating system**
31 | Which operating system and version are you using?
32 | You can use the command `lsb_release -a` to get it.
33 | 
34 | **GCC**
35 | What version of GCC are you using?
36 | You can use the command `gcc -v` to get it.
37 | 
38 | **Python**
39 | What version of Python are you using?
40 | You can use the command `python --version` to get it.
41 | 
42 | **NextDenovo**
43 | What version of NextDenovo are you using?
44 | You can use the command `nextDenovo -v` to get it.
45 | 
46 | **To Reproduce** (Optional)
47 | Steps to reproduce the behavior. Providing a minimal test dataset on which we can reproduce the behavior will generally lead to quicker turnaround time!
48 | 
49 | **Additional context** (Optional)
50 | Add any other context about the problem here.
51 | 


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/question-or-feature-request-.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | name: 'Question or Feature request '
 3 | about: Ask a question or suggest an idea for this project
 4 | title: ''
 5 | labels: ''
 6 | assignees: ''
 7 | 
 8 | ---
 9 | 
10 | **Question or Expected behavior**
11 | A clear and concise description of your question or what you expected to happen.
12 | 
13 | **Operating system**
14 | Which operating system and version are you using?
15 | You can use the command `lsb_release -a` to get it.
16 | 
17 | **GCC**
18 | What version of GCC are you using?
19 | You can use the command `gcc -v` to get it.
20 | 
21 | **Python**
22 | What version of Python are you using?
23 | You can use the command `python --version` to get it.
24 | 
25 | **NextDenovo**
26 | What version of NextDenovo are you using?
27 | You can use the command `nextDenovo -v` to get it.
28 | 
29 | **Additional context** (Optional)
30 | Add any other context about the problem here.
31 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
  1 | # Byte-compiled / optimized / DLL files
  2 | __pycache__/
  3 | *.py[cod]
  4 | *$py.class
  5 | 
  6 | # C extensions
  7 | *.so
  8 | 
  9 | # Distribution / packaging
 10 | .Python
 11 | build/
 12 | develop-eggs/
 13 | dist/
 14 | downloads/
 15 | eggs/
 16 | .eggs/
 17 | lib64/
 18 | parts/
 19 | sdist/
 20 | var/
 21 | wheels/
 22 | *.egg-info/
 23 | .installed.cfg
 24 | *.egg
 25 | MANIFEST
 26 | 
 27 | # PyInstaller
 28 | #  Usually these files are written by a python script from a template
 29 | #  before PyInstaller builds the exe, so as to inject date/other infos into it.
 30 | *.manifest
 31 | *.spec
 32 | 
 33 | # Installer logs
 34 | pip-log.txt
 35 | pip-delete-this-directory.txt
 36 | 
 37 | # Unit test / coverage reports
 38 | htmlcov/
 39 | .tox/
 40 | .coverage
 41 | .coverage.*
 42 | .cache
 43 | nosetests.xml
 44 | coverage.xml
 45 | *.cover
 46 | .hypothesis/
 47 | .pytest_cache/
 48 | 
 49 | # Translations
 50 | *.mo
 51 | *.pot
 52 | 
 53 | # Django stuff:
 54 | *.log
 55 | local_settings.py
 56 | db.sqlite3
 57 | 
 58 | # Flask stuff:
 59 | instance/
 60 | .webassets-cache
 61 | 
 62 | # Scrapy stuff:
 63 | .scrapy
 64 | 
 65 | # Sphinx documentation
 66 | docs/_build/
 67 | 
 68 | # PyBuilder
 69 | target/
 70 | 
 71 | # Jupyter Notebook
 72 | .ipynb_checkpoints
 73 | 
 74 | # pyenv
 75 | .python-version
 76 | 
 77 | # celery beat schedule file
 78 | celerybeat-schedule
 79 | 
 80 | # SageMath parsed files
 81 | *.sage.py
 82 | 
 83 | # Environments
 84 | .env
 85 | .venv
 86 | env/
 87 | venv/
 88 | ENV/
 89 | env.bak/
 90 | venv.bak/
 91 | 
 92 | # Spyder project settings
 93 | .spyderproject
 94 | .spyproject
 95 | 
 96 | # Rope project settings
 97 | .ropeproject
 98 | 
 99 | # mkdocs documentation
100 | /site
101 | 
102 | # mypy
103 | .mypy_cache/
104 | 
105 | 


--------------------------------------------------------------------------------
/.readthedocs.yaml:
--------------------------------------------------------------------------------
 1 | # .readthedocs.yaml
 2 | # Read the Docs configuration file
 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 4 | 
 5 | # Required
 6 | version: 2
 7 | 
 8 | # Set the version of Python and other tools you might need
 9 | build:
10 |   os: ubuntu-22.04
11 |   tools:
12 |     python: "3.11"
13 | 
14 | # Build documentation in the docs/ directory with Sphinx
15 | sphinx:
16 |   configuration: doc/conf.py
17 | 
18 | # We recommend specifying your dependencies to enable reproducible builds:
19 | # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
20 | python:
21 |   install:
22 |   - requirements: doc/requirements.txt


--------------------------------------------------------------------------------
/Makefile:
--------------------------------------------------------------------------------
 1 | TOP_DIR=$(PWD)
 2 | BIN_DIR=$(TOP_DIR)/bin
 3 | SUB_DIR=minimap2 util lib
 4 | 
 5 | TARGET_MINIMAP=minimap2-nd
 6 | TARGER_UTIL=seq_dump ovl_sort seq_stat ovl_cvt seq_bit bam_sort nextgraph
 7 | 
 8 | all:make_bin_dir
 9 | 	$(foreach N, $(SUB_DIR), make -C $(N);)
10 | 	cp $(TOP_DIR)/minimap2/$(TARGET_MINIMAP) $(TOP_DIR)/bin/
11 | 	$(foreach N, $(TARGER_UTIL), cp $(TOP_DIR)/util/$(N) $(TOP_DIR)/bin/;)
12 | 
13 | make_bin_dir:
14 | 	@if test ! -d $(BIN_DIR) ; \
15 | 	then \
16 | 		mkdir $(BIN_DIR) ; \
17 | 	fi
18 | 
19 | clean:
20 | 	rm -rf $(BIN_DIR)
21 | 	$(foreach N, $(SUB_DIR), make -C $(N) clean;)
22 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | [![Downloads](https://img.shields.io/github/downloads/Nextomics/NextDenovo/total?logo=github)](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz)
 2 | [![Release](https://img.shields.io/github/release/Nextomics/NextDenovo.svg)](https://github.com/Nextomics/NextDenovo/releases)
 3 | [![Documentation Status](https://readthedocs.org/projects/nextdenovo/badge/?version=latest)](https://nextdenovo.readthedocs.io/en/latest/?badge=latest)
 4 | [![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs13059--024--03252--4-blue)](https://doi.org/10.1186/s13059-024-03252-4)
 5 | 
 6 | # NextDenovo
 7 | NextDenovo is a string graph-based *de novo* assembler for long reads (CLR, ~~HiFi~~ and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, try [NextPolish](https://github.com/Nextomics/NextPolish).
 8 | 
 9 | We benchmarked NextDenovo against other assemblers using Oxford Nanopore long reads from [human](https://nextdenovo.readthedocs.io/en/latest/TEST2.html) and [Drosophila melanogaster](https://nextdenovo.readthedocs.io/en/latest/TEST4.html), and PacBio continuous long reads (CLR) from [Arabidopsis thaliana](https://nextdenovo.readthedocs.io/en/latest/TEST3.html). NextDenovo produces more contiguous assemblies with fewer contigs compared to the other tools. NextDenovo also shows a high assembly accurate level in terms of assembly consistency and single-base accuracy.
10 | 
11 | ## Installation
12 | 
13 | * **REQUIREMENT**
14 | 	* [Python](https://www.python.org/download/releases/) (Support python 2 and 3):
15 | 		* [Paralleltask](https://github.com/moold/ParallelTask) `pip install paralleltask`
16 | 
17 | * **INSTALL**  
18 | 
19 | 	click [here](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz) or use the following command:   
20 | 	```sh
21 | 	wget https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz
22 | 	tar -vxzf NextDenovo.tgz && cd NextDenovo
23 | 	```   
24 | 
25 | 	If you want to compile from the source, run:
26 | 
27 | 	```sh
28 | 	git clone git@github.com:Nextomics/NextDenovo.git
29 | 	cd NextDenovo && make
30 | 	```
31 | 
32 | * **TEST**  
33 | `nextDenovo test_data/run.cfg`
34 | 
35 | ## Learn
36 | 
37 | * [Quick Start](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#quick-start) - no experience required, download and assemble now
38 | * [Tutorial](https://nextdenovo.readthedocs.io/en/latest/TEST1.html) - step by step introduction to assemble the HG002 genome
39 | * [FAQ](https://nextdenovo.readthedocs.io/en/latest/FAQ.html) - frequently asked questions
40 | * [Parameter Reference](https://nextdenovo.readthedocs.io/en/latest/OPTION.html) - a detailed introduction about all the parameters
41 | * [Cite](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#cite) - if you get a good assembly with NextDenovo, please cite it
42 | 
43 | ## Star
44 | 
45 | You can track updates by tab the `Star` button on the upper-right corner at this page.
46 | 
47 | ## More
48 | 
49 | The complete user documentation is available [here](https://nextdenovo.readthedocs.io/en/latest/).
50 | 


--------------------------------------------------------------------------------
/VERSION:
--------------------------------------------------------------------------------
1 | 2.5.2
2 | 


--------------------------------------------------------------------------------
/doc/TEST1.rst:
--------------------------------------------------------------------------------
 1 | .. title:: Tutorial
 2 | 
 3 | Assemble the genome of HG002_NA24385_son using NextDenovo
 4 | -----------------------------------------------------------
 5 | 
 6 | 1. **Download reads**
 7 | 
 8 |   .. code-block:: shell
 9 | 
10 |     wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/guppy-V2.3.4_2019-06-26/ultra-long-ont.fastq.gz
11 | 
12 | 2. **Prepare input file (input.fofn)**
13 | 
14 |    .. code-block:: shell
15 | 
16 |     ls ultra-long-ont.fastq.gz > input.fofn
17 | 
18 | 3. **Prepare config file (run.cfg)** 
19 | 
20 |   .. code-block:: shell
21 | 
22 |     [General]
23 |     job_type = sge # here we use SGE to manage jobs
24 |     job_prefix = nextDenovo
25 |     task = all
26 |     rewrite = yes
27 |     deltmp = yes 
28 |     parallel_jobs = 22
29 |     input_type = raw
30 |     read_type = ont # clr, ont, hifi
31 |     input_fofn = input.fofn
32 |     workdir = HG002_NA24385_son_assemble
33 | 
34 |     [correct_option]
35 |     read_cutoff = 1k
36 |     genome_size = 3g # estimated genome size
37 |     sort_options = -m 50g -t 30
38 |     minimap2_options_raw = -t 8
39 |     pa_correction = 5
40 |     correction_options = -p 30
41 | 
42 |     [assemble_option]
43 |     minimap2_options_cns = -t 8 
44 |     nextgraph_options = -a 1 
45 | 
46 | 4. **Run**
47 | 
48 |   .. code-block:: shell
49 |     
50 |     nohup nextDenovo run.cfg &
51 | 
52 | 5. **Get result**
53 | 
54 |   - Final corrected reads file (use the ``-b`` parameter to get more corrected reads)::
55 |   
56 |       HG002_NA24385_son_assemble/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta
57 | 
58 |   - Final assembly result::
59 |   
60 |       HG002_NA24385_son_assemble/03.ctg_graph/nd.asm.fasta
61 | 
62 |   you can get some basic statistical information from file ``HG002_NA24385_son_assemble/03.ctg_graph/nd.asm.fasta.stat``, the folowing is the assembly statistics with default parameters::   
63 | 
64 |     Type           Length (bp)            Count (#)
65 |     N10            168924870                   2
66 |     N20            127260938                   4
67 |     N30             94622851                   7
68 |     N40             85456034                  10
69 |     N50             79737202                  13
70 |     N60             69943198                  17
71 |     N70             58504138                  21
72 |     N80             40548231                  27
73 |     N90             19732879                  36
74 | 
75 |     Min.               82439                   -
76 |     Max.           220056807                   -
77 |     Ave.            24389616                   -
78 |     Total         2877974703                 118
79 | 
80 |   .. note:: This result will have some minor changes with the version upgrade.


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/doc/TEST2.pdf:
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https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/doc/TEST2.pdf


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/doc/TEST3.pdf:
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https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/doc/TEST3.pdf


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/doc/TEST4.pdf:
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https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/doc/TEST4.pdf


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/doc/conf.py:
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 1 | # Configuration file for the Sphinx documentation builder.
 2 | #
 3 | # This file only contains a selection of the most common options. For a full
 4 | # list see the documentation:
 5 | # https://www.sphinx-doc.org/en/master/usage/configuration.html
 6 | 
 7 | # -- Path setup --------------------------------------------------------------
 8 | 
 9 | # If extensions (or modules to document with autodoc) are in another directory,
10 | # add these directories to sys.path here. If the directory is relative to the
11 | # documentation root, use os.path.abspath to make it absolute, like shown here.
12 | #
13 | # import os
14 | # import sys
15 | # sys.path.insert(0, os.path.abspath('.'))
16 | 
17 | 
18 | # -- Project information -----------------------------------------------------
19 | 
20 | project = 'nextdenovo'
21 | copyright = '2020, jiang'
22 | author = 'jiang'
23 | 
24 | 
25 | # -- General configuration ---------------------------------------------------
26 | 
27 | # Add any Sphinx extension module names here, as strings. They can be
28 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
29 | # ones.
30 | extensions = [
31 | 	'sphinx_copybutton',
32 | 	'sphinx_rtd_theme',
33 | ]
34 | 
35 | # Add any paths that contain templates here, relative to this directory.
36 | templates_path = ['_templates']
37 | 
38 | # List of patterns, relative to source directory, that match files and
39 | # directories to ignore when looking for source files.
40 | # This pattern also affects html_static_path and html_extra_path.
41 | exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
42 | 
43 | 
44 | # -- Options for HTML output -------------------------------------------------
45 | 
46 | # The theme to use for HTML and HTML Help pages.  See the documentation for
47 | # a list of builtin themes.
48 | #
49 | html_theme = 'sphinx_rtd_theme'
50 | 
51 | # Add any paths that contain custom static files (such as style sheets) here,
52 | # relative to this directory. They are copied after the builtin static files,
53 | # so a file named "default.css" will overwrite the builtin "default.css".
54 | html_static_path = ['_static']
55 | 


--------------------------------------------------------------------------------
/doc/index.rst:
--------------------------------------------------------------------------------
 1 | .. toctree::
 2 |   :caption: Getting started
 3 |   :maxdepth: 2
 4 |   :hidden:
 5 |   
 6 |   Usuage <QSTART>
 7 |   Tutorial <TEST1>   
 8 |   Parameter Reference <OPTION>     
 9 |   Utilities <UTILITY>
10 |   FAQ <FAQ>
11 | 
12 | .. toctree::
13 |   :caption: Benchmark
14 |   :maxdepth: 2
15 |   :hidden:
16 | 
17 |   CHM13hTERT human cell line with 120x Oxford Nanopore data <TEST2>   
18 |   Arabidopsis thaliana with 192X PacBio CLR data (~1% heterozygosity) <TEST3>   
19 |   Drosophila melanogaster with 69X Oxford Nanopore data <TEST4>
20 |   More data <TEST5>
21 | 
22 | .. include:: QSTART.rst


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/doc/requirements.txt:
--------------------------------------------------------------------------------
1 | sphinx_copybutton==0.5.2
2 | sphinx_rtd_theme==1.1.1


--------------------------------------------------------------------------------
/doc/run.cfg:
--------------------------------------------------------------------------------
 1 | [General]
 2 | job_type = local # local, slurm, sge, pbs, lsf
 3 | job_prefix = nextDenovo
 4 | task = all # all, correct, assemble
 5 | rewrite = yes # yes/no
 6 | deltmp = yes 
 7 | parallel_jobs = 20 # number of tasks used to run in parallel
 8 | input_type = raw # raw, corrected
 9 | read_type = clr # clr, ont, hifi
10 | input_fofn = input.fofn
11 | workdir = 01_rundir
12 | 
13 | [correct_option]
14 | read_cutoff = 1k
15 | genome_size = 1g # estimated genome size
16 | sort_options = -m 20g -t 15
17 | minimap2_options_raw = -t 8
18 | pa_correction = 3 # number of corrected tasks used to run in parallel, each corrected task requires ~TOTAL_INPUT_BASES/4 bytes of memory usage.
19 | correction_options = -p 15
20 | 
21 | [assemble_option]
22 | minimap2_options_cns = -t 8 
23 | nextgraph_options = -a 1
24 | 
25 | # see https://nextdenovo.readthedocs.io/en/latest/OPTION.html for a detailed introduction about all the parameters
26 | 
27 | 


--------------------------------------------------------------------------------
/lib/Makefile:
--------------------------------------------------------------------------------
 1 | CC=gcc
 2 | CFLAGS = -std=c99 -O3 -Wall -Wno-unused-function
 3 | FPIC = -fPIC -shared
 4 | HTSDIR = ./htslib/
 5 | LIB_OBJECT = nextcorrect.so ovlseq.so ctg_cns.so ckit.so
 6 | CTG_CNS_CFLAGS = -D_SVID_SOURCE -DLGS_CORRECT -I $(HTSDIR) -lcurl -lcrypto -lm -lpthread -lz $(HTSLIB_CFLAGS)
 7 | 
 8 | all: $(LIB_OBJECT)
 9 | 
10 | $(HTSDIR)/libhts.a:
11 | 	cd  $(HTSDIR) && ./configure --disable-bz2 --disable-lzma
12 | 	@+make -C $(HTSDIR) CPPFLAGS+=-fPIC $(INCLUDES)
13 | 
14 | nextcorrect.so: align.c dag.c nextcorrect.c
15 | 	$(CC) $(CFLAGS) $(FPIC) $(INCLUDES) -o $@ $^ 
16 | 
17 | ovlseq.so: ovlseq.c bseq.c ovl.c index.c
18 | 	$(CC) $(CFLAGS) $(FPIC) $(INCLUDES) -o $@ $^ -lz
19 | 
20 | nextcorrect: align.c dag.c nextcorrect.c
21 | 	$(CC) $(CFLAGS) -o $@ $^
22 | 
23 | ctg_cns.so: bseq.c align.c bsort.c dag.c ctg_cns.c $(HTSDIR)/libhts.a
24 | 	$(CC) $(CFLAGS) $(FPIC) $(INCLUDES) -o $@ $^ $(CTG_CNS_CFLAGS) 
25 | 
26 | ckit.so: kit.c bseq.c
27 | 	$(CC) $(CFLAGS) $(FPIC) $(INCLUDES) -o $@ $^ -lz
28 | 
29 | ckit: kit.c bseq.c
30 | 	$(CC) $(CFLAGS) -o $@ $^ -lz
31 | 
32 | ctg_cns: bseq.c align.c dag.c bsort.c ctg_cns.c $(HTSDIR)/libhts.a
33 | 	$(CC) $(CFLAGS) $(INCLUDES) -o $@ $^ $(CTG_CNS_CFLAGS)
34 | 
35 | ovlseq: ovlseq.c bseq.c ovl.c index.c
36 | 	$(CC) $(CFLAGS) -lz -Wno-unused-function -o $@ $^
37 | 
38 | clean:
39 | 	rm -rf *.o *.pyc $(LIB_OBJECT) nextcorrect ovlseq nextcorrect ctg_cns kit __pycache__
40 | 	@+make clean -C $(HTSDIR)
41 | 


--------------------------------------------------------------------------------
/lib/align.h:
--------------------------------------------------------------------------------
 1 | #include <stdbool.h>
 2 | #include <stdlib.h>
 3 | #include <string.h>
 4 | #include <inttypes.h>
 5 | #include <stdio.h>
 6 | 
 7 | 
 8 | #ifdef LGS_CORRECT
 9 |     typedef struct {
10 |         unsigned int shift;
11 |         unsigned int aln_len;
12 |             unsigned int max_aln_len;
13 |         unsigned int aln_t_s;
14 |         unsigned int aln_t_e;//not include
15 |         unsigned int aln_t_len;
16 |         unsigned int aln_q_s;
17 |         unsigned int aln_q_e;//not include
18 |         unsigned int aln_q_len;
19 |         char * q_aln_str;
20 |         char * t_aln_str;
21 |     } alignment;
22 | #else
23 |     typedef struct {
24 |         unsigned int shift;
25 |         unsigned int aln_len;
26 |         unsigned int aln_t_s;
27 |         unsigned int aln_t_e;//not include
28 |         unsigned int aln_t_len;
29 |         unsigned int aln_q_len;//not include
30 |         char * q_aln_str;
31 |         char * t_aln_str;
32 |     } alignment;
33 | #endif
34 | 
35 | 
36 | typedef struct {
37 |     unsigned int aln_len; //align len
38 |     unsigned int aln_mlen;//match len
39 |     unsigned int aln_t_s;
40 |     unsigned int aln_t_e;//not include
41 |     unsigned int aln_q_s;
42 |     unsigned int aln_q_e;//not include
43 | } alignpos;
44 | 
45 | void malloc_vd(int **V, uint8_t ***D, uint64_t max_mem_d);
46 | void clean_V(int *V, int max_mem_d);
47 | void destory_vd(int *V, uint8_t **D);
48 | void revcomp_bseq(char *str, int len);
49 | void str_tolower(char *p);
50 | void str_toupper(char *p);
51 | void ide(const char *query_seq, int q_len, const char *target_seq, int t_len,
52 | 	int *V, uint8_t **D, int max_d, int band_size, int *mlen, int *blen);
53 | void alnpos(const char *query_seq, int q_len, const char *target_seq, int t_len,
54 |     int *V, uint8_t **D, int max_d, int band_size, alignpos *aln);
55 | void extend_fwd(const char *query_seq, int q_len, const char *target_seq, int t_len,
56 | 	int *V, uint8_t **D, int max_d, int band_size, float d_factor, int *bstx, int *bsty);
57 | void extend_rev(const char *query_seq, int q_len, const char *target_seq, int t_len,
58 | 	int *V, uint8_t **D, int max_d, int band_size, float d_factor, int *bstx, int *bsty);
59 | void align_hq(char *query_seq, int q_len, char *target_seq, int t_len, 
60 | 	alignment *align_rtn, int *V, uint8_t **D);
61 | void align(char *query_seq, int q_len, char *target_seq, int t_len, 
62 | 	alignment *align_rtn, int *V, uint8_t **D);
63 | 


--------------------------------------------------------------------------------
/lib/bseq.h:
--------------------------------------------------------------------------------
 1 | #include <zlib.h>
 2 | #include "mseq.h"
 3 | KSEQ_INIT(gzFile, gzread)
 4 | 
 5 | typedef struct {
 6 | 	char *seq;
 7 | 	char *buffer;
 8 | 	char **bases_arr;
 9 | 	uint32_t *tmp;
10 | 	uint32_t m;
11 | } sbbuf;
12 | 
13 | int init_seq_mode(FILE *fp);
14 | uint32_t seq2bit(FILE *fp, uint32_t name, uint32_t len, char *seq);
15 | void seq2bit1(uint32_t *s, uint32_t len, char *seq);
16 | void bit2seq1(uint32_t *s, uint32_t len, char *seq);
17 | sbbuf *init_sbbuf(uint32_t len);
18 | void destroy_sbbbuf(sbbuf *buf);
19 | void subbit(sbbuf *buf, FILE *fp, int rev, uint64_t offset, uint32_t start, uint32_t end);
20 | void subbit_(sbbuf *buf, uint32_t *fp, int rev, uint64_t offset, uint32_t start, uint32_t end);
21 | void subfa(sbbuf *buf, FILE *fp, int rev, uint64_t offset, uint32_t start, uint32_t end);
22 | int kseq_r(kseq_t *seq);
23 | 


--------------------------------------------------------------------------------
/lib/bsort.h:
--------------------------------------------------------------------------------
 1 | #ifndef BAM_SORT
 2 | #define BAM_SORT
 3 | 
 4 | #include "htslib/ksort.h"
 5 | #include "htslib/hts_os.h"
 6 | #include "htslib/khash.h"
 7 | #include "htslib/klist.h"
 8 | #include "htslib/kstring.h"
 9 | #include "htslib/sam.h"
10 | 
11 | #define SAM_GLOBAL_ARGS_INIT {{0},{0}}
12 | 
13 | typedef struct sam_global_args {
14 |     htsFormat in; 
15 |     htsFormat out;
16 |     char *reference;
17 |     int nthreads;
18 |     int write_index;
19 | } sam_global_args;
20 | 
21 | 
22 | typedef struct bam1_tag {
23 |     bam1_t *bam_record;
24 |     union {
25 |         const uint8_t *tag;
26 |         uint64_t pos;
27 |     } u;
28 | } bam1_tag;
29 | 
30 | typedef struct heap1_t{
31 |     int i;
32 |     uint32_t rev;
33 |     uint64_t pos, idx;
34 |     bam1_tag entry;
35 | } heap1_t;
36 | 
37 | typedef struct {
38 |     int n, init;
39 |     struct heap1_t *heap;
40 |     struct trans_tbl *translation_tbl;
41 |     hts_itr_t **iter;
42 |     samFile **fp;
43 |     bam_hdr_t **hdr;
44 |     char** fn;
45 |     uint64_t idx;
46 | } bam_merge_iter;
47 | 
48 | int bam_merge_iter_init(int, char*,const char *, const char *, bam_merge_iter *);
49 | int bam_merge_iter_core(bam_merge_iter *);
50 | int bam_merge_iter_destroy(bam_merge_iter *);
51 | int bam_sort_core_ext(int, char*, const char *, const char *, const char *, 
52 |     const char *,size_t, int, const htsFormat *, const htsFormat *);
53 | void sam_global_args_free(sam_global_args *);
54 | 
55 | #endif
56 | 


--------------------------------------------------------------------------------
/lib/htslib/README:
--------------------------------------------------------------------------------
1 | HTSlib is an implementation of a unified C library for accessing common file
2 | formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
3 | data.  It is the core library used by samtools and bcftools.
4 | 
5 | See INSTALL for building and installation instructions.
6 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/cram.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | Copyright (c) 2012-2013 Genome Research Ltd.
 3 | Author: James Bonfield <jkb@sanger.ac.uk>
 4 | 
 5 | Redistribution and use in source and binary forms, with or without
 6 | modification, are permitted provided that the following conditions are met:
 7 | 
 8 |    1. Redistributions of source code must retain the above copyright notice,
 9 | this list of conditions and the following disclaimer.
10 | 
11 |    2. Redistributions in binary form must reproduce the above copyright notice,
12 | this list of conditions and the following disclaimer in the documentation
13 | and/or other materials provided with the distribution.
14 | 
15 |    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 | Institute nor the names of its contributors may be used to endorse or promote
17 | products derived from this software without specific prior written permission.
18 | 
19 | THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 | DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 | */
30 | 
31 | /*! \file
32 |  * CRAM interface.
33 |  *
34 |  * Consider using the higher level hts_*() API for programs that wish to
35 |  * be file format agnostic (see htslib/hts.h).
36 |  *
37 |  * This API should be used for CRAM specific code. The specifics of the
38 |  * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
39 |  * although these should not be included directly (use this file instead).
40 |  */
41 | 
42 | #ifndef _CRAM_H_
43 | #define _CRAM_H_
44 | 
45 | #include "cram/cram_samtools.h"
46 | #include "cram/sam_header.h"
47 | #include "cram_structs.h"
48 | #include "cram_io.h"
49 | #include "cram_encode.h"
50 | #include "cram_decode.h"
51 | #include "cram_stats.h"
52 | #include "cram_codecs.h"
53 | #include "cram_index.h"
54 | 
55 | // Validate against the external cram.h,
56 | //
57 | // This contains duplicated portions from cram_io.h and cram_structs.h,
58 | // so we want to ensure that the prototypes match.
59 | #include "htslib/cram.h"
60 | 
61 | #endif
62 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/cram_stats.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | Copyright (c) 2012-2013 Genome Research Ltd.
 3 | Author: James Bonfield <jkb@sanger.ac.uk>
 4 | 
 5 | Redistribution and use in source and binary forms, with or without
 6 | modification, are permitted provided that the following conditions are met:
 7 | 
 8 |    1. Redistributions of source code must retain the above copyright notice,
 9 | this list of conditions and the following disclaimer.
10 | 
11 |    2. Redistributions in binary form must reproduce the above copyright notice,
12 | this list of conditions and the following disclaimer in the documentation
13 | and/or other materials provided with the distribution.
14 | 
15 |    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 | Institute nor the names of its contributors may be used to endorse or promote
17 | products derived from this software without specific prior written permission.
18 | 
19 | THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 | DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 | */
30 | 
31 | #ifndef _CRAM_STATS_H_
32 | #define _CRAM_STATS_H_
33 | 
34 | #ifdef __cplusplus
35 | extern "C" {
36 | #endif
37 | 
38 | cram_stats *cram_stats_create(void);
39 | void cram_stats_add(cram_stats *st, int32_t val);
40 | void cram_stats_del(cram_stats *st, int32_t val);
41 | void cram_stats_dump(cram_stats *st);
42 | void cram_stats_free(cram_stats *st);
43 | 
44 | /*
45 |  * Computes entropy from integer frequencies for various encoding methods and
46 |  * picks the best encoding.
47 |  *
48 |  * FIXME: we could reuse some of the code here for the actual encoding
49 |  * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
50 |  *
51 |  * Returns the best codec to use.
52 |  */
53 | enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st);
54 | 
55 | #ifdef __cplusplus
56 | }
57 | #endif
58 | 
59 | #endif
60 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/files.c:
--------------------------------------------------------------------------------
 1 | /*
 2 | Copyright (c) 1994, 1996-1997, 2000, 2003 MEDICAL RESEARCH COUNCIL
 3 | All rights reserved
 4 | 
 5 | Redistribution and use in source and binary forms, with or without
 6 | modification, are permitted provided that the following conditions are met:
 7 | 
 8 |    1 Redistributions of source code must retain the above copyright notice,
 9 | this list of conditions and the following disclaimer.
10 | 
11 |    2 Redistributions in binary form must reproduce the above copyright notice,
12 | this list of conditions and the following disclaimer in the documentation
13 | and/or other materials provided with the distribution.
14 | 
15 |    3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
16 | MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
17 | promote products derived from this software without specific prior written
18 | permission.
19 | 
20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
21 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
22 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
24 | ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
25 | (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
26 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
27 | ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
28 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
29 | SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30 |  */
31 | 
32 | #include <config.h>
33 | 
34 | #include "cram/misc.h"
35 | 
36 | #include <sys/types.h>
37 | #include <sys/stat.h>
38 | /* Alliant's Concentrix <sys/stat.h> is hugely deficient */
39 | /* Define things we require in this program              */
40 | /* Methinks S_IFMT and S_IFDIR aren't defined in POSIX   */
41 | #ifndef S_ISDIR
42 | #define S_ISDIR(m)      (((m)&S_IFMT) == S_IFDIR)
43 | #endif /*!S_ISDIR*/
44 | #ifndef S_ISREG
45 | #define S_ISREG(m)      (((m)&S_IFMT) == S_IFREG)
46 | #endif /*!S_ISREG*/
47 | 
48 | int is_directory(char * fn)
49 | {
50 |     struct stat buf;
51 |     if ( stat(fn,&buf) ) return 0;
52 |     return S_ISDIR(buf.st_mode);
53 | }
54 | 
55 | int is_file(char * fn)
56 | {
57 |     struct stat buf;
58 |     if ( stat(fn,&buf) ) return 0;
59 |     return S_ISREG(buf.st_mode);
60 | }
61 | 
62 | int file_exists(char * fn)
63 | {
64 |     struct stat buf;
65 |     return ( stat(fn,&buf) == 0);
66 | }
67 | 
68 | int file_size(char * fn)
69 | {
70 |     struct stat buf;
71 |     if ( stat(fn,&buf) != 0) return 0;
72 |     return buf.st_size;
73 | }
74 | 
75 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/mFILE.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | Copyright (c) 2005-2006, 2008-2009 Genome Research Ltd.
 3 | Author: James Bonfield <jkb@sanger.ac.uk>
 4 | 
 5 | Redistribution and use in source and binary forms, with or without
 6 | modification, are permitted provided that the following conditions are met:
 7 | 
 8 |    1. Redistributions of source code must retain the above copyright notice,
 9 | this list of conditions and the following disclaimer.
10 | 
11 |    2. Redistributions in binary form must reproduce the above copyright notice,
12 | this list of conditions and the following disclaimer in the documentation
13 | and/or other materials provided with the distribution.
14 | 
15 |    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 | Institute nor the names of its contributors may be used to endorse or promote
17 | products derived from this software without specific prior written permission.
18 | 
19 | THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 | DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 | */
30 | 
31 | #ifndef _MFILE_H_
32 | #define _MFILE_H_
33 | 
34 | #include <stdio.h>
35 | 
36 | #ifdef __cplusplus
37 | extern "C" {
38 | #endif
39 | 
40 | typedef struct {
41 |     FILE *fp;
42 |     char *data;
43 |     size_t alloced;
44 |     int eof;
45 |     int mode; /* open mode in MF_?? define bit pattern */
46 |     size_t size;
47 |     size_t offset;
48 |     size_t flush_pos;
49 | } mFILE;
50 | 
51 | // Work around a clash with winuser.h
52 | #ifdef MF_APPEND
53 | #  undef MF_APPEND
54 | #endif
55 | 
56 | #define MF_READ    1
57 | #define MF_WRITE   2
58 | #define MF_APPEND  4
59 | #define MF_BINARY  8
60 | #define MF_TRUNC  16
61 | #define MF_MODEX  32
62 | #define MF_MMAP   64
63 | 
64 | mFILE *mfreopen(const char *path, const char *mode, FILE *fp);
65 | mFILE *mfopen(const char *path, const char *mode);
66 | int mfdetach(mFILE *mf);
67 | int mfclose(mFILE *mf);
68 | int mfdestroy(mFILE *mf);
69 | int mfseek(mFILE *mf, long offset, int whence);
70 | long mftell(mFILE *mf);
71 | void mrewind(mFILE *mf);
72 | void mftruncate(mFILE *mf, long offset);
73 | int mfeof(mFILE *mf);
74 | size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf);
75 | size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf);
76 | int mfgetc(mFILE *mf);
77 | int mungetc(int c, mFILE *mf);
78 | mFILE *mfcreate(char *data, int size);
79 | mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp);
80 | void mfrecreate(mFILE *mf, char *data, int size);
81 | void *mfsteal(mFILE *mf, size_t *size_out);
82 | char *mfgets(char *s, int size, mFILE *mf);
83 | int mfflush(mFILE *mf);
84 | mFILE *mstdin(void);
85 | mFILE *mstdout(void);
86 | mFILE *mstderr(void);
87 | void mfascii(mFILE *mf);
88 | 
89 | #ifdef __cplusplus
90 | }
91 | #endif
92 | 
93 | #endif /* _MFILE_H_ */
94 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/pooled_alloc.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | Copyright (c) 2009 Genome Research Ltd.
 3 | Author: Rob Davies <rmd@sanger.ac.uk>
 4 | 
 5 | Redistribution and use in source and binary forms, with or without
 6 | modification, are permitted provided that the following conditions are met:
 7 | 
 8 |    1. Redistributions of source code must retain the above copyright notice,
 9 | this list of conditions and the following disclaimer.
10 | 
11 |    2. Redistributions in binary form must reproduce the above copyright notice,
12 | this list of conditions and the following disclaimer in the documentation
13 | and/or other materials provided with the distribution.
14 | 
15 |    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 | Institute nor the names of its contributors may be used to endorse or promote
17 | products derived from this software without specific prior written permission.
18 | 
19 | THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 | DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 | */
30 | 
31 | #ifndef _POOLED_ALLOC_H_
32 | #define _POOLED_ALLOC_H_
33 | 
34 | #include <stddef.h>
35 | 
36 | #ifdef __cplusplus
37 | extern "C" {
38 | #endif
39 | 
40 | /*
41 |  * Implements a pooled block allocator where all items are the same size,
42 |  * but we need many of them.
43 |  */
44 | typedef struct {
45 |     void   *pool;
46 |     size_t  used;
47 | } pool_t;
48 | 
49 | typedef struct {
50 |     size_t dsize;
51 |     size_t psize;
52 |     size_t npools;
53 |     pool_t *pools;
54 |     void *free;
55 | } pool_alloc_t;
56 | 
57 | pool_alloc_t *pool_create(size_t dsize);
58 | void pool_destroy(pool_alloc_t *p);
59 | void *pool_alloc(pool_alloc_t *p);
60 | void pool_free(pool_alloc_t *p, void *ptr);
61 | 
62 | #ifdef __cplusplus
63 | }
64 | #endif
65 | 
66 | #endif /*_POOLED_ALLOC_H_*/
67 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/rANS_static.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * Copyright (c) 2014 Genome Research Ltd.
 3 |  * Author(s): James Bonfield
 4 |  *
 5 |  * Redistribution and use in source and binary forms, with or without
 6 |  * modification, are permitted provided that the following conditions are met:
 7 |  *
 8 |  *    1. Redistributions of source code must retain the above copyright notice,
 9 |  *       this list of conditions and the following disclaimer.
10 |  *
11 |  *    2. Redistributions in binary form must reproduce the above
12 |  *       copyright notice, this list of conditions and the following
13 |  *       disclaimer in the documentation and/or other materials provided
14 |  *       with the distribution.
15 |  *
16 |  *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
17 |  *       Institute nor the names of its contributors may be used to endorse
18 |  *       or promote products derived from this software without specific
19 |  *       prior written permission.
20 |  *
21 |  * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
22 |  * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
23 |  * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
24 |  * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
25 |  * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
26 |  * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
27 |  * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
28 |  * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
29 |  * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
30 |  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
31 |  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
32 |  */
33 | 
34 | 
35 | #ifndef RANS_STATIC_H
36 | #define RANS_STATIC_H
37 | 
38 | #ifdef __cplusplus
39 | extern "C" {
40 | #endif
41 | 
42 | unsigned char *rans_compress(unsigned char *in, unsigned int in_size,
43 |                              unsigned int *out_size, int order);
44 | unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size,
45 |                                unsigned int *out_size);
46 | 
47 | #ifdef __cplusplus
48 | }
49 | #endif
50 | 
51 | #endif /* RANS_STATIC_H */
52 | 


--------------------------------------------------------------------------------
/lib/htslib/cram/string_alloc.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | Copyright (c) 2010 Genome Research Ltd.
 3 | Author: Andrew Whitwham <aw7@sanger.ac.uk>
 4 | 
 5 | Redistribution and use in source and binary forms, with or without
 6 | modification, are permitted provided that the following conditions are met:
 7 | 
 8 |    1. Redistributions of source code must retain the above copyright notice,
 9 | this list of conditions and the following disclaimer.
10 | 
11 |    2. Redistributions in binary form must reproduce the above copyright notice,
12 | this list of conditions and the following disclaimer in the documentation
13 | and/or other materials provided with the distribution.
14 | 
15 |    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 | Institute nor the names of its contributors may be used to endorse or promote
17 | products derived from this software without specific prior written permission.
18 | 
19 | THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 | DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 | */
30 | 
31 | #ifndef _STRING_ALLOC_H_
32 | #define _STRING_ALLOC_H_
33 | 
34 | #include <stdlib.h>
35 | 
36 | #ifdef __cplusplus
37 | extern "C" {
38 | #endif
39 | 
40 | /*
41 |  * A pooled string allocator intended to cut down on the
42 |  * memory overhead of many small string allocations.
43 |  *
44 |  * Andrew Whitwham, September 2010.
45 |  */
46 | 
47 | typedef struct {
48 |     char *str;
49 |     size_t used;
50 | } string_t;
51 | 
52 | typedef struct {
53 |     size_t max_length;
54 |     size_t nstrings;
55 |     string_t *strings;
56 | } string_alloc_t;
57 | 
58 | string_alloc_t *string_pool_create(size_t max_length);
59 | void string_pool_destroy(string_alloc_t *a_str);
60 | char *string_alloc(string_alloc_t *a_str, size_t length);
61 | char *string_dup(string_alloc_t *a_str, char *instr);
62 | char *string_ndup(string_alloc_t *a_str, char *instr, size_t len);
63 | 
64 | #ifdef __cplusplus
65 | }
66 | #endif
67 | 
68 | #endif
69 | 


--------------------------------------------------------------------------------
/lib/htslib/hts_internal.h:
--------------------------------------------------------------------------------
 1 | /*  hts_internal.h -- internal functions; not part of the public API.
 2 | 
 3 |     Copyright (C) 2015-2016 Genome Research Ltd.
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in
13 | all copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | DEALINGS IN THE SOFTWARE.  */
22 | 
23 | #ifndef HTSLIB_HTS_INTERNAL_H
24 | #define HTSLIB_HTS_INTERNAL_H
25 | 
26 | #include <stddef.h>
27 | #include <ctype.h>
28 | 
29 | #include "htslib/hts.h"
30 | 
31 | #include "textutils_internal.h"
32 | 
33 | #ifdef __cplusplus
34 | extern "C" {
35 | #endif
36 | 
37 | struct hFILE;
38 | 
39 | struct hts_json_token {
40 |     char type;    ///< Token type
41 |     char *str;    ///< Value as a C string (filled in for all token types)
42 |     // TODO Add other fields to fill in for particular data types, e.g.
43 |     // int inum;
44 |     // float fnum;
45 | };
46 | 
47 | struct cram_fd;
48 | 
49 | char *hts_idx_getfn(const char *fn, const char *ext);
50 | 
51 | // The CRAM implementation stores the loaded index within the cram_fd rather
52 | // than separately as is done elsewhere in htslib.  So if p is a pointer to
53 | // an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an
54 | // hts_cram_idx_t and should be cast accordingly.
55 | typedef struct hts_cram_idx_t {
56 |     int fmt;
57 |     struct cram_fd *cram;
58 | } hts_cram_idx_t;
59 | 
60 | 
61 | // Entry point to hFILE_multipart backend.
62 | struct hFILE *hopen_htsget_redirect(struct hFILE *hfile, const char *mode);
63 | 
64 | struct hts_path_itr {
65 |     kstring_t path, entry;
66 |     void *dirv;  // DIR * privately
67 |     const char *pathdir, *prefix, *suffix;
68 |     size_t prefix_len, suffix_len, entry_dir_l;
69 | };
70 | 
71 | void hts_path_itr_setup(struct hts_path_itr *itr, const char *path,
72 |     const char *builtin_path, const char *prefix, size_t prefix_len,
73 |     const char *suffix, size_t suffix_len);
74 | 
75 | const char *hts_path_itr_next(struct hts_path_itr *itr);
76 | 
77 | void *load_plugin(void **pluginp, const char *filename, const char *symbol);
78 | void *plugin_sym(void *plugin, const char *name, const char **errmsg);
79 | void close_plugin(void *plugin);
80 | 
81 | #ifdef __cplusplus
82 | }
83 | #endif
84 | 
85 | #endif
86 | 


--------------------------------------------------------------------------------
/lib/htslib/hts_os.c:
--------------------------------------------------------------------------------
 1 | /// @file hts_os.c
 2 | /// Operating System specific tweaks, for compatibility with POSIX.
 3 | /*
 4 |    Copyright (C) 2017 Genome Research Ltd.
 5 | 
 6 |     Author: James Bonfield <jkb@sanger.ac.uk>
 7 | 
 8 | Permission is hereby granted, free of charge, to any person obtaining a copy
 9 | of this software and associated documentation files (the "Software"), to deal
10 | in the Software without restriction, including without limitation the rights
11 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12 | copies of the Software, and to permit persons to whom the Software is
13 | furnished to do so, subject to the following conditions:
14 | 
15 | The above copyright notice and this permission notice shall be included in
16 | all copies or substantial portions of the Software.
17 | 
18 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
21 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
23 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
24 | DEALINGS IN THE SOFTWARE.  */
25 | 
26 | #include <config.h>
27 | 
28 | // Windows (maybe more) lack a drand48 implementation.
29 | #ifndef HAVE_DRAND48
30 | #include "os/rand.c"
31 | #else
32 | #include <stdlib.h>
33 | void hts_srand48(long seed) { srand48(seed); }
34 | double hts_erand48(unsigned short xseed[3]) { return erand48(xseed); }
35 | double hts_drand48(void) { return drand48(); }
36 | double hts_lrand48(void) { return lrand48(); }
37 | #endif
38 | 
39 | // // On Windows when using the MSYS or Cygwin terminals, isatty fails
40 | // #ifdef _WIN32
41 | // #define USE_FILEEXTD
42 | // #include "os/iscygpty.c"
43 | // #endif
44 | 


--------------------------------------------------------------------------------
/lib/htslib/htsfile.1:
--------------------------------------------------------------------------------
 1 | .TH htsfile 1 "18 July 2018" "htslib-1.9" "Bioinformatics tools"
 2 | .SH NAME
 3 | htsfile \- identify high-throughput sequencing data files
 4 | .\"
 5 | .\" Copyright (C) 2015, 2017 Genome Research Ltd.
 6 | .\"
 7 | .\" Author: John Marshall <jm18@sanger.ac.uk>
 8 | .\"
 9 | .\" Permission is hereby granted, free of charge, to any person obtaining a
10 | .\" copy of this software and associated documentation files (the "Software"),
11 | .\" to deal in the Software without restriction, including without limitation
12 | .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
13 | .\" and/or sell copies of the Software, and to permit persons to whom the
14 | .\" Software is furnished to do so, subject to the following conditions:
15 | .\"
16 | .\" The above copyright notice and this permission notice shall be included in
17 | .\" all copies or substantial portions of the Software.
18 | .\"
19 | .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
20 | .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
21 | .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
22 | .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
23 | .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
24 | .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
25 | .\" DEALINGS IN THE SOFTWARE.
26 | .\"
27 | .SH SYNOPSIS
28 | .B htsfile
29 | .RB [ -chHv ]
30 | .IR FILE ...
31 | .SH DESCRIPTION
32 | The \fBhtsfile\fR utility attempts to identify what kind of high-throughput
33 | sequencing data files the specified files are, and provides minimal viewing
34 | capabilities for some kinds of data file.
35 | .P
36 | It can identify sequencing data files such as SAM, BAM, and CRAM;
37 | variant calling data files such as VCF and BCF;
38 | index files used to index these data files;
39 | and compressed versions of many of them.
40 | .P
41 | For each \fIFILE\fR given, \fBhtsfile\fP prints a description of the file
42 | format determined, using similar keyword conventions to \fBfile\fP(1):
43 | "text" indicates a textual file that can probably be viewed on a terminal;
44 | "data" indicates binary data;
45 | "sequence", "variant calling", and "index" indicate different categories of
46 | data file.
47 | When it can be identified, the name of the particular file format (such as
48 | "BAM" or "VCF") is printed at the start of the description.
49 | .P
50 | When used to view file contents as text, \fBhtsfile\fP can optionally show
51 | only headers or only data records, but has no other filtering capabilities.
52 | Use \fBsamtools\fR or \fBbcftools\fR if you need more extensive viewing or
53 | filtering capabilities.
54 | .P
55 | The following options are accepted:
56 | .TP 4n
57 | .BR -c ", " --view
58 | Instead of identifying the specified files, display a textual representation
59 | of their contents on standard output.
60 | .IP
61 | By default, \fB--view\fR refuses to display files in unknown formats.
62 | When \fB--verbose\fR is also given, the raw contents of such files are
63 | displayed, with non-printable characters shown via C-style "\\x" hexadecimal
64 | escape sequences.
65 | .TP
66 | .BR -h ", " --header-only
67 | Display data file headers only.
68 | Implies \fB--view\fR.
69 | .TP
70 | .BR -H ", " --no-header
71 | When viewing files, display data records only.
72 | .TP
73 | .BR -v ", " --verbose
74 | Display additional warnings and diagnostic messages.
75 | Using \fB--verbose\fR repeatedly further raises the verbosity.
76 | .PP
77 | .SH SEE ALSO
78 | .IR bcftools (1),
79 | .IR file (1),
80 | .IR samtools (1)
81 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib.pc.in:
--------------------------------------------------------------------------------
 1 | includedir=@-includedir@
 2 | libdir=@-libdir@
 3 | 
 4 | # Flags and libraries needed when linking against a static libhts.a
 5 | # (used by manual and semi-manual pkg-config(1)-style enquiries).
 6 | static_ldflags=@static_LDFLAGS@
 7 | static_libs=@static_LIBS@
 8 | 
 9 | Name: htslib
10 | Description: C library for high-throughput sequencing data formats
11 | Version: @-PACKAGE_VERSION@
12 | Cflags: -I${includedir}
13 | Libs: -L${libdir} -lhts
14 | Libs.private: -L${libdir} @private_LIBS@ -lhts -lm -lpthread
15 | Requires.private: zlib @pc_requires@
16 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib/hts_defs.h:
--------------------------------------------------------------------------------
 1 | /*  hts_defs.h -- Miscellaneous definitions.
 2 | 
 3 |     Copyright (C) 2013-2015,2017 Genome Research Ltd.
 4 | 
 5 |     Author: John Marshall <jm18@sanger.ac.uk>
 6 | 
 7 | Permission is hereby granted, free of charge, to any person obtaining a copy
 8 | of this software and associated documentation files (the "Software"), to deal
 9 | in the Software without restriction, including without limitation the rights
10 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 | copies of the Software, and to permit persons to whom the Software is
12 | furnished to do so, subject to the following conditions:
13 | 
14 | The above copyright notice and this permission notice shall be included in
15 | all copies or substantial portions of the Software.
16 | 
17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 | DEALINGS IN THE SOFTWARE.  */
24 | 
25 | #ifndef HTSLIB_HTS_DEFS_H
26 | #define HTSLIB_HTS_DEFS_H
27 | 
28 | #ifdef __clang__
29 | #ifdef __has_attribute
30 | #define HTS_COMPILER_HAS(attribute) __has_attribute(attribute)
31 | #endif
32 | 
33 | #elif defined __GNUC__
34 | #define HTS_GCC_AT_LEAST(major, minor) \
35 |     (__GNUC__ > (major) || (__GNUC__ == (major) && __GNUC_MINOR__ >= (minor)))
36 | #endif
37 | 
38 | #ifndef HTS_COMPILER_HAS
39 | #define HTS_COMPILER_HAS(attribute) 0
40 | #endif
41 | #ifndef HTS_GCC_AT_LEAST
42 | #define HTS_GCC_AT_LEAST(major, minor) 0
43 | #endif
44 | 
45 | #if HTS_COMPILER_HAS(__noreturn__) || HTS_GCC_AT_LEAST(3,0)
46 | #define HTS_NORETURN __attribute__ ((__noreturn__))
47 | #else
48 | #define HTS_NORETURN
49 | #endif
50 | 
51 | // GCC introduced warn_unused_result in 3.4 but added -Wno-unused-result later
52 | #if HTS_COMPILER_HAS(__warn_unused_result__) || HTS_GCC_AT_LEAST(4,5)
53 | #define HTS_RESULT_USED __attribute__ ((__warn_unused_result__))
54 | #else
55 | #define HTS_RESULT_USED
56 | #endif
57 | 
58 | #if HTS_COMPILER_HAS(__unused__) || HTS_GCC_AT_LEAST(3,0)
59 | #define HTS_UNUSED __attribute__ ((__unused__))
60 | #else
61 | #define HTS_UNUSED
62 | #endif
63 | 
64 | #if HTS_COMPILER_HAS(__deprecated__) || HTS_GCC_AT_LEAST(4,5)
65 | #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
66 | #elif HTS_GCC_AT_LEAST(3,1)
67 | #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__))
68 | #else
69 | #define HTS_DEPRECATED(message)
70 | #endif
71 | 
72 | #if HTS_COMPILER_HAS(__deprecated__) || HTS_GCC_AT_LEAST(6,4)
73 | #define HTS_DEPRECATED_ENUM(message) __attribute__ ((__deprecated__ (message)))
74 | #else
75 | #define HTS_DEPRECATED_ENUM(message)
76 | #endif
77 | 
78 | // On mingw the "printf" format type doesn't work.  It needs "gnu_printf"
79 | // in order to check %lld and %z, otherwise it defaults to checking against
80 | // the Microsoft library printf format options despite linking against the
81 | // GNU posix implementation of printf.  The __MINGW_PRINTF_FORMAT macro
82 | // expands to printf or gnu_printf as required, but obviously may not
83 | // exist
84 | #ifdef __MINGW_PRINTF_FORMAT
85 | #define HTS_PRINTF_FMT __MINGW_PRINTF_FORMAT
86 | #else
87 | #define HTS_PRINTF_FMT printf
88 | #endif
89 | 
90 | #if HTS_COMPILER_HAS(__format__) || HTS_GCC_AT_LEAST(3,0)
91 | #define HTS_FORMAT(type, idx, first) __attribute__((__format__ (type, idx, first)))
92 | #else
93 | #define HTS_FORMAT(type, idx, first)
94 | #endif
95 | 
96 | #endif
97 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib/hts_os.h:
--------------------------------------------------------------------------------
 1 | /// @file hts_os.h
 2 | /// Operating System specific tweaks, for compatibility with POSIX.
 3 | /*
 4 |    Copyright (C) 2017 Genome Research Ltd.
 5 | 
 6 |     Author: James Bonfield <jkb@sanger.ac.uk>
 7 | 
 8 | Permission is hereby granted, free of charge, to any person obtaining a copy
 9 | of this software and associated documentation files (the "Software"), to deal
10 | in the Software without restriction, including without limitation the rights
11 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12 | copies of the Software, and to permit persons to whom the Software is
13 | furnished to do so, subject to the following conditions:
14 | 
15 | The above copyright notice and this permission notice shall be included in
16 | all copies or substantial portions of the Software.
17 | 
18 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
21 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
23 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
24 | DEALINGS IN THE SOFTWARE.  */
25 | 
26 | #ifndef HTSLIB_HTS_OS_H
27 | #define HTSLIB_HTS_OS_H
28 | 
29 | extern void hts_srand48(long seed);
30 | extern double hts_erand48(unsigned short xseed[3]);
31 | extern double hts_drand48(void);
32 | extern long hts_lrand48(void);
33 | 
34 | #if defined(_WIN32) && !defined(__CYGWIN__)
35 | // Windows usually lacks *rand48(), but cygwin provides them.
36 | #define srand48(S) hts_srand48((S))
37 | #define erand48(X) hts_erand48((X))
38 | #define drand48() hts_drand48()
39 | #define lrand48() hts_lrand48()
40 | #endif
41 | 
42 | #if 0  /* def _WIN32 - disabled for now, not currently used */
43 | /* Check if the fd is a cygwin/msys's pty. */
44 | extern int is_cygpty(int fd);
45 | #endif
46 | 
47 | 
48 | #if defined(__MINGW32__)
49 | #include <io.h>
50 | #define mkdir(filename,mode) mkdir((filename))
51 | #endif
52 | 
53 | #ifdef _WIN32
54 | #include <stdlib.h>
55 | #define srandom srand
56 | #define random rand
57 | #endif
58 | 
59 | #endif
60 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib/kfunc.h:
--------------------------------------------------------------------------------
 1 | /* The MIT License
 2 | 
 3 |    Copyright (C) 2010, 2013 Genome Research Ltd.
 4 |    Copyright (C) 2011 Attractive Chaos <attractor@live.co.uk>
 5 | 
 6 |    Permission is hereby granted, free of charge, to any person obtaining
 7 |    a copy of this software and associated documentation files (the
 8 |    "Software"), to deal in the Software without restriction, including
 9 |    without limitation the rights to use, copy, modify, merge, publish,
10 |    distribute, sublicense, and/or sell copies of the Software, and to
11 |    permit persons to whom the Software is furnished to do so, subject to
12 |    the following conditions:
13 | 
14 |    The above copyright notice and this permission notice shall be
15 |    included in all copies or substantial portions of the Software.
16 | 
17 |    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
18 |    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
19 |    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
20 |    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
21 |    BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
22 |    ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
23 |    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
24 |    SOFTWARE.
25 | */
26 | 
27 | #ifndef HTSLIB_KFUNC_H
28 | #define HTSLIB_KFUNC_H
29 | 
30 | #ifdef __cplusplus
31 | extern "C" {
32 | #endif
33 | 
34 | /* Log gamma function
35 |  * \log{\Gamma(z)}
36 |  * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
37 |  */
38 | double kf_lgamma(double z);
39 | 
40 | /* complementary error function
41 |  * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
42 |  * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
43 |  */
44 | double kf_erfc(double x);
45 | 
46 | /* The following computes regularized incomplete gamma functions.
47 |  * Formulas are taken from Wiki, with additional input from Numerical
48 |  * Recipes in C (for modified Lentz's algorithm) and AS245
49 |  * (http://lib.stat.cmu.edu/apstat/245).
50 |  *
51 |  * A good online calculator is available at:
52 |  *
53 |  *   http://www.danielsoper.com/statcalc/calc23.aspx
54 |  *
55 |  * It calculates upper incomplete gamma function, which equals
56 |  * kf_gammaq(s,z)*tgamma(s).
57 |  */
58 | 
59 | double kf_gammap(double s, double z);
60 | double kf_gammaq(double s, double z);
61 | 
62 | /* Regularized incomplete beta function. The method is taken from
63 |  * Numerical Recipe in C, 2nd edition, section 6.4. The following web
64 |  * page calculates the incomplete beta function, which equals
65 |  * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
66 |  *
67 |  *   http://www.danielsoper.com/statcalc/calc36.aspx
68 |  */
69 | double kf_betai(double a, double b, double x);
70 | 
71 | /*
72 |  *    n11  n12  | n1_
73 |  *    n21  n22  | n2_
74 |  *   -----------+----
75 |  *    n_1  n_2  | n
76 |  */
77 | double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
78 | 
79 | #ifdef __cplusplus
80 | }
81 | #endif
82 | 
83 | #endif
84 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib/knetfile.h:
--------------------------------------------------------------------------------
  1 | /* The MIT License
  2 | 
  3 |    Copyright (c) 2008 by Genome Research Ltd (GRL).
  4 |                  2010 by Attractive Chaos <attractor@live.co.uk>
  5 | 
  6 |    Permission is hereby granted, free of charge, to any person obtaining
  7 |    a copy of this software and associated documentation files (the
  8 |    "Software"), to deal in the Software without restriction, including
  9 |    without limitation the rights to use, copy, modify, merge, publish,
 10 |    distribute, sublicense, and/or sell copies of the Software, and to
 11 |    permit persons to whom the Software is furnished to do so, subject to
 12 |    the following conditions:
 13 | 
 14 |    The above copyright notice and this permission notice shall be
 15 |    included in all copies or substantial portions of the Software.
 16 | 
 17 |    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 18 |    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 19 |    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 20 |    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
 21 |    BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
 22 |    ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 23 |    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 24 |    SOFTWARE.
 25 | */
 26 | 
 27 | #ifndef KNETFILE_H
 28 | #define KNETFILE_H
 29 | 
 30 | #include <stdint.h>
 31 | #include <fcntl.h>
 32 | #include <sys/types.h>
 33 | 
 34 | #ifndef _WIN32
 35 | #define netread(fd, ptr, len) read(fd, ptr, len)
 36 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
 37 | #define netclose(fd) close(fd)
 38 | #else
 39 | #include <winsock2.h>
 40 | #define netread(fd, ptr, len) recv(fd, ptr, len, 0)
 41 | #define netwrite(fd, ptr, len) send(fd, ptr, len, 0)
 42 | #define netclose(fd) closesocket(fd)
 43 | #endif
 44 | 
 45 | // FIXME: currently I/O is unbuffered
 46 | 
 47 | #define KNF_TYPE_LOCAL 1
 48 | #define KNF_TYPE_FTP   2
 49 | #define KNF_TYPE_HTTP  3
 50 | 
 51 | typedef struct knetFile_s {
 52 | 	int type, fd;
 53 | 	int64_t offset;
 54 | 	char *host, *port;
 55 | 
 56 | 	// the following are for FTP only
 57 | 	int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
 58 | 	char *response, *retr, *size_cmd;
 59 | 	int64_t seek_offset; // for lazy seek
 60 |     int64_t file_size;
 61 | 
 62 | 	// the following are for HTTP only
 63 | 	char *path, *http_host;
 64 | } knetFile;
 65 | 
 66 | #define knet_tell(fp) ((fp)->offset)
 67 | #define knet_fileno(fp) ((fp)->fd)
 68 | 
 69 | #ifdef __cplusplus
 70 | extern "C" {
 71 | #endif
 72 | 
 73 | #ifdef _WIN32
 74 | 	int knet_win32_init();
 75 | 	void knet_win32_destroy();
 76 | #endif
 77 | 
 78 | 	knetFile *knet_open(const char *fn, const char *mode);
 79 | 
 80 | 	/*
 81 | 	   This only works with local files.
 82 | 	 */
 83 | 	knetFile *knet_dopen(int fd, const char *mode);
 84 | 
 85 | 	/*
 86 | 	  If ->is_ready==0, this routine updates ->fd; otherwise, it simply
 87 | 	  reads from ->fd.
 88 | 	 */
 89 | 	ssize_t knet_read(knetFile *fp, void *buf, size_t len);
 90 | 
 91 | 	/*
 92 | 	  This routine only sets ->offset and ->is_ready=0. It does not
 93 | 	  communicate with the FTP server.
 94 | 	 */
 95 | 	off_t knet_seek(knetFile *fp, off_t off, int whence);
 96 | 	int knet_close(knetFile *fp);
 97 | 
 98 | #ifdef __cplusplus
 99 | }
100 | #endif
101 | 
102 | #endif
103 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib/tbx.h:
--------------------------------------------------------------------------------
 1 | /// @file htslib/tbx.h
 2 | /// Tabix API functions.
 3 | /*
 4 |     Copyright (C) 2009, 2012-2015 Genome Research Ltd.
 5 |     Copyright (C) 2010, 2012 Broad Institute.
 6 | 
 7 |     Author: Heng Li <lh3@sanger.ac.uk>
 8 | 
 9 | Permission is hereby granted, free of charge, to any person obtaining a copy
10 | of this software and associated documentation files (the "Software"), to deal
11 | in the Software without restriction, including without limitation the rights
12 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
13 | copies of the Software, and to permit persons to whom the Software is
14 | furnished to do so, subject to the following conditions:
15 | 
16 | The above copyright notice and this permission notice shall be included in
17 | all copies or substantial portions of the Software.
18 | 
19 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
20 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
21 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
22 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
23 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
24 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
25 | DEALINGS IN THE SOFTWARE.  */
26 | 
27 | #ifndef HTSLIB_TBX_H
28 | #define HTSLIB_TBX_H
29 | 
30 | #include "hts.h"
31 | 
32 | #ifdef __cplusplus
33 | extern "C" {
34 | #endif
35 | 
36 | #define TBX_MAX_SHIFT 31
37 | 
38 | #define TBX_GENERIC 0
39 | #define TBX_SAM     1
40 | #define TBX_VCF     2
41 | #define TBX_UCSC    0x10000
42 | 
43 | typedef struct {
44 |     int32_t preset;
45 |     int32_t sc, bc, ec; // seq col., beg col. and end col.
46 |     int32_t meta_char, line_skip;
47 | } tbx_conf_t;
48 | 
49 | typedef struct {
50 |     tbx_conf_t conf;
51 |     hts_idx_t *idx;
52 |     void *dict;
53 | } tbx_t;
54 | 
55 | extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf;
56 | 
57 |     #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
58 |     #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
59 |     #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
60 |     #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
61 |     #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx))
62 | 
63 |     int tbx_name2id(tbx_t *tbx, const char *ss);
64 | 
65 |     /* Internal helper function used by tbx_itr_next() */
66 |     BGZF *hts_get_bgzfp(htsFile *fp);
67 |     int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end);
68 | 
69 |     tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf);
70 |     int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf);
71 |     int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
72 |     int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf);
73 |     tbx_t *tbx_index_load(const char *fn);
74 |     tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
75 |     const char **tbx_seqnames(tbx_t *tbx, int *n);  // free the array but not the values
76 |     void tbx_destroy(tbx_t *tbx);
77 | 
78 | #ifdef __cplusplus
79 | }
80 | #endif
81 | 
82 | #endif
83 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib/vcf_sweep.h:
--------------------------------------------------------------------------------
 1 | /// @file htslib/vcf_sweep.h
 2 | /// Forward/reverse sweep API.
 3 | /*
 4 |     Copyright (C) 2013 Genome Research Ltd.
 5 | 
 6 |     Author: Petr Danecek <pd3@sanger.ac.uk>
 7 | 
 8 | Permission is hereby granted, free of charge, to any person obtaining a copy
 9 | of this software and associated documentation files (the "Software"), to deal
10 | in the Software without restriction, including without limitation the rights
11 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12 | copies of the Software, and to permit persons to whom the Software is
13 | furnished to do so, subject to the following conditions:
14 | 
15 | The above copyright notice and this permission notice shall be included in
16 | all copies or substantial portions of the Software.
17 | 
18 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
21 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
23 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
24 | DEALINGS IN THE SOFTWARE.  */
25 | 
26 | #ifndef HTSLIB_VCF_SWEEP_H
27 | #define HTSLIB_VCF_SWEEP_H
28 | 
29 | #include "hts.h"
30 | #include "vcf.h"
31 | 
32 | #ifdef __cplusplus
33 | extern "C" {
34 | #endif
35 | 
36 | typedef struct _bcf_sweep_t bcf_sweep_t;
37 | 
38 | bcf_sweep_t *bcf_sweep_init(const char *fname);
39 | void bcf_sweep_destroy(bcf_sweep_t *sw);
40 | bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw);
41 | bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw);
42 | bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw);
43 | 
44 | #ifdef __cplusplus
45 | }
46 | #endif
47 | 
48 | #endif
49 | 


--------------------------------------------------------------------------------
/lib/htslib/htslib_vars.mk:
--------------------------------------------------------------------------------
 1 | # Makefile variables useful for third-party code using htslib's public API.
 2 | #
 3 | #    Copyright (C) 2013-2017 Genome Research Ltd.
 4 | #
 5 | #    Author: John Marshall <jm18@sanger.ac.uk>
 6 | #
 7 | # Permission is hereby granted, free of charge, to any person obtaining a copy
 8 | # of this software and associated documentation files (the "Software"), to deal
 9 | # in the Software without restriction, including without limitation the rights
10 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 | # copies of the Software, and to permit persons to whom the Software is
12 | # furnished to do so, subject to the following conditions:
13 | #
14 | # The above copyright notice and this permission notice shall be included in
15 | # all copies or substantial portions of the Software.
16 | #
17 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 | # DEALINGS IN THE SOFTWARE.
24 | 
25 | # These variables can be used to express dependencies on htslib headers.
26 | # See htslib.mk for details.
27 | 
28 | htslib_bgzf_h = $(HTSPREFIX)htslib/bgzf.h $(htslib_hts_defs_h)
29 | htslib_cram_h = $(HTSPREFIX)htslib/cram.h $(htslib_hts_h)
30 | htslib_faidx_h = $(HTSPREFIX)htslib/faidx.h $(htslib_hts_defs_h)
31 | htslib_hfile_h = $(HTSPREFIX)htslib/hfile.h $(htslib_hts_defs_h)
32 | htslib_hts_h = $(HTSPREFIX)htslib/hts.h $(htslib_hts_defs_h) $(htslib_hts_log_h)
33 | htslib_hts_defs_h = $(HTSPREFIX)htslib/hts_defs.h
34 | htslib_hts_endian_h = $(HTSPREFIX)htslib/hts_endian.h
35 | htslib_hts_log_h = $(HTSPREFIX)htslib/hts_log.h $(htslib_hts_defs_h)
36 | htslib_hts_os_h = $(HTSPREFIX)htslib/hts_os.h
37 | htslib_kbitset_h = $(HTSPREFIX)htslib/kbitset.h
38 | htslib_kfunc_h = $(HTSPREFIX)htslib/kfunc.h
39 | htslib_khash_h = $(HTSPREFIX)htslib/khash.h
40 | htslib_khash_str2int_h = $(HTSPREFIX)htslib/khash_str2int.h $(htslib_khash_h)
41 | htslib_klist_h = $(HTSPREFIX)htslib/klist.h
42 | htslib_knetfile_h = $(HTSPREFIX)htslib/knetfile.h
43 | htslib_kseq_h = $(HTSPREFIX)htslib/kseq.h
44 | htslib_ksort_h = $(HTSPREFIX)htslib/ksort.h
45 | htslib_kstring_h = $(HTSPREFIX)htslib/kstring.h
46 | htslib_regidx_h = $(HTSPREFIX)htslib/regidx.h
47 | htslib_sam_h = $(HTSPREFIX)htslib/sam.h $(htslib_hts_h)
48 | htslib_synced_bcf_reader_h = $(HTSPREFIX)htslib/synced_bcf_reader.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_tbx_h)
49 | htslib_tbx_h = $(HTSPREFIX)htslib/tbx.h $(htslib_hts_h)
50 | htslib_thread_pool_h = $(HTSPREFIX)htslib/thread_pool.h
51 | htslib_vcf_h = $(HTSPREFIX)htslib/vcf.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_hts_defs_h) $(htslib_hts_endian_h)
52 | htslib_vcf_sweep_h = $(HTSPREFIX)htslib/vcf_sweep.h $(htslib_hts_h) $(htslib_vcf_h)
53 | htslib_vcfutils_h = $(HTSPREFIX)htslib/vcfutils.h $(htslib_vcf_h)
54 | 


--------------------------------------------------------------------------------
/lib/htslib/os/lzma_stub.h:
--------------------------------------------------------------------------------
 1 | #ifndef LZMA_STUB_H
 2 | #define LZMA_STUB_H
 3 | 
 4 | /* Some platforms, notably macOS, ship a usable liblzma shared library but
 5 |    do not ship any LZMA header files. The <lzma.h> and <lzma/{*}.h> header
 6 |    files that come with the library contain the following statement:
 7 | 
 8 |      *
 9 |      * Author: Lasse Collin
10 |      *
11 |      * This file has been put into the public domain.
12 |      * You can do whatever you want with this file.
13 |      *
14 | 
15 |    Accordingly the following declarations have been copied and distilled
16 |    from <lzma/base.h> and <lzma/container.h> (primarily) and are sufficient
17 |    to compile cram/cram_io.c in the absence of proper LZMA headers.
18 | 
19 |    This file, lzma_stub.h, remains in the public domain.  */
20 | 
21 | #include <stdint.h>
22 | 
23 | #ifdef __cplusplus
24 | extern "C" {
25 | #endif
26 | 
27 | typedef enum { LZMA_OK = 0, LZMA_STREAM_END = 1 } lzma_ret;
28 | typedef enum { LZMA_RUN = 0, LZMA_FINISH = 3 } lzma_action;
29 | typedef enum { LZMA_CHECK_CRC32 = 1 } lzma_check;
30 | typedef enum { LZMA_RESERVED_ENUM = 0 } lzma_reserved_enum;
31 | 
32 | struct lzma_allocator;
33 | struct lzma_internal;
34 | 
35 | typedef struct {
36 |     const uint8_t *next_in;
37 |     size_t avail_in;
38 |     uint64_t total_in;
39 | 
40 |     uint8_t *next_out;
41 |     size_t avail_out;
42 |     uint64_t total_out;
43 | 
44 |     const struct lzma_allocator *allocator;
45 |     struct lzma_internal *internal;
46 | 
47 |     void *reserved_ptr1;
48 |     void *reserved_ptr2;
49 |     void *reserved_ptr3;
50 |     void *reserved_ptr4;
51 |     uint64_t reserved_int1;
52 |     uint64_t reserved_int2;
53 |     size_t reserved_int3;
54 |     size_t reserved_int4;
55 |     lzma_reserved_enum reserved_enum1;
56 |     lzma_reserved_enum reserved_enum2;
57 | } lzma_stream;
58 | 
59 | #define LZMA_STREAM_INIT \
60 |     { NULL, 0, 0, NULL, 0, 0, NULL, NULL, \
61 |     NULL, NULL, NULL, NULL, 0, 0, 0, 0, \
62 |     LZMA_RESERVED_ENUM, LZMA_RESERVED_ENUM }
63 | 
64 | extern size_t lzma_stream_buffer_bound(size_t uncompressed_size);
65 | 
66 | extern lzma_ret lzma_easy_buffer_encode(
67 |         uint32_t preset, lzma_check check,
68 |         const struct lzma_allocator *allocator,
69 |         const uint8_t *in, size_t in_size,
70 |         uint8_t *out, size_t *out_pos, size_t out_size);
71 | 
72 | extern lzma_ret lzma_stream_decoder(
73 |         lzma_stream *strm, uint64_t memlimit, uint32_t flags);
74 | 
75 | extern uint64_t lzma_easy_decoder_memusage(uint32_t preset);
76 | 
77 | extern lzma_ret lzma_code(lzma_stream *strm, lzma_action action);
78 | 
79 | extern void lzma_end(lzma_stream *strm);
80 | 
81 | #ifdef __cplusplus
82 | }
83 | #endif
84 | 
85 | #endif
86 | 


--------------------------------------------------------------------------------
/lib/htslib/os/rand.c:
--------------------------------------------------------------------------------
 1 | /*  rand.c -- drand48 implementation from the FreeBSD source tree. */
 2 | 
 3 | // This file is an amalgamation of the many small files in FreeBSD to do with
 4 | // drand48 and friends implementations.
 5 | // It comprises _rand48.c, rand48.h, srand48.c, drand48.c, erand48.c, lrand48.c
 6 | 
 7 | /*
 8 |  * Copyright (c) 1993 Martin Birgmeier
 9 |  * All rights reserved.
10 |  *
11 |  * You may redistribute unmodified or modified versions of this source
12 |  * code provided that the above copyright notice and this and the
13 |  * following conditions are retained.
14 |  *
15 |  * This software is provided ``as is'', and comes with no warranties
16 |  * of any kind. I shall in no event be liable for anything that happens
17 |  * to anyone/anything when using this software.
18 |  */
19 | 
20 | //#include <sys/cdefs.h>
21 | //__FBSDID("$FreeBSD: src/lib/libc/gen/_rand48.c,v 1.2 2002/03/22 21:52:05 obrien Exp $");
22 | 
23 | #include <math.h>
24 | 
25 | #define	RAND48_SEED_0	(0x330e)
26 | #define	RAND48_SEED_1	(0xabcd)
27 | #define	RAND48_SEED_2	(0x1234)
28 | #define	RAND48_MULT_0	(0xe66d)
29 | #define	RAND48_MULT_1	(0xdeec)
30 | #define	RAND48_MULT_2	(0x0005)
31 | #define	RAND48_ADD	(0x000b)
32 | 
33 | static unsigned short _rand48_seed[3] = {
34 | 	RAND48_SEED_0,
35 | 	RAND48_SEED_1,
36 | 	RAND48_SEED_2
37 | };
38 | static unsigned short _rand48_mult[3] = {
39 | 	RAND48_MULT_0,
40 | 	RAND48_MULT_1,
41 | 	RAND48_MULT_2
42 | };
43 | static unsigned short _rand48_add = RAND48_ADD;
44 | 
45 | static void
46 | _dorand48(unsigned short xseed[3])
47 | {
48 | 	unsigned long accu;
49 | 	unsigned short temp[2];
50 | 
51 | 	accu = (unsigned long) _rand48_mult[0] * (unsigned long) xseed[0] +
52 | 	 (unsigned long) _rand48_add;
53 | 	temp[0] = (unsigned short) accu;	/* lower 16 bits */
54 | 	accu >>= sizeof(unsigned short) * 8;
55 | 	accu += (unsigned long) _rand48_mult[0] * (unsigned long) xseed[1] +
56 | 	 (unsigned long) _rand48_mult[1] * (unsigned long) xseed[0];
57 | 	temp[1] = (unsigned short) accu;	/* middle 16 bits */
58 | 	accu >>= sizeof(unsigned short) * 8;
59 | 	accu += _rand48_mult[0] * xseed[2] + _rand48_mult[1] * xseed[1] + _rand48_mult[2] * xseed[0];
60 | 	xseed[0] = temp[0];
61 | 	xseed[1] = temp[1];
62 | 	xseed[2] = (unsigned short) accu;
63 | }
64 | 
65 | void
66 | hts_srand48(long seed)
67 | {
68 | 	_rand48_seed[0] = RAND48_SEED_0;
69 | 	_rand48_seed[1] = (unsigned short) seed;
70 | 	_rand48_seed[2] = (unsigned short) (seed >> 16);
71 | 	_rand48_mult[0] = RAND48_MULT_0;
72 | 	_rand48_mult[1] = RAND48_MULT_1;
73 | 	_rand48_mult[2] = RAND48_MULT_2;
74 | 	_rand48_add = RAND48_ADD;
75 | }
76 | 
77 | double
78 | hts_erand48(unsigned short xseed[3])
79 | {
80 | 	_dorand48(xseed);
81 | 	return ldexp((double) xseed[0], -48) +
82 | 	       ldexp((double) xseed[1], -32) +
83 | 	       ldexp((double) xseed[2], -16);
84 | }
85 | 
86 | double
87 | hts_drand48(void)
88 | {
89 | 	return hts_erand48(_rand48_seed);
90 | }
91 | 
92 | long
93 | hts_lrand48(void)
94 | {
95 | 	_dorand48(_rand48_seed);
96 | 	return ((long) _rand48_seed[2] << 15) + ((long) _rand48_seed[1] >> 1);
97 | }
98 | 


--------------------------------------------------------------------------------
/lib/htslib/sam.5:
--------------------------------------------------------------------------------
 1 | '\" t
 2 | .TH sam 5 "August 2013" "htslib" "Bioinformatics formats"
 3 | .SH NAME
 4 | sam \- Sequence Alignment/Map file format
 5 | .\"
 6 | .\" Copyright (C) 2009, 2013 Genome Research Ltd.
 7 | .\"
 8 | .\" Author: Heng Li <lh3@sanger.ac.uk>
 9 | .\"
10 | .\" Permission is hereby granted, free of charge, to any person obtaining a
11 | .\" copy of this software and associated documentation files (the "Software"),
12 | .\" to deal in the Software without restriction, including without limitation
13 | .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
14 | .\" and/or sell copies of the Software, and to permit persons to whom the
15 | .\" Software is furnished to do so, subject to the following conditions:
16 | .\"
17 | .\" The above copyright notice and this permission notice shall be included in
18 | .\" all copies or substantial portions of the Software.
19 | .\"
20 | .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
21 | .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
22 | .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
23 | .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
24 | .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
25 | .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
26 | .\" DEALINGS IN THE SOFTWARE.
27 | .\"
28 | .SH DESCRIPTION
29 | Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started
30 | with the `@' symbol, each alignment line consists of:
31 | .TS
32 | nlbl.
33 | 1	QNAME	Query template/pair NAME
34 | 2	FLAG	bitwise FLAG
35 | 3	RNAME	Reference sequence NAME
36 | 4	POS	1-based leftmost POSition/coordinate of clipped sequence
37 | 5	MAPQ	MAPping Quality (Phred-scaled)
38 | 6	CIGAR	extended CIGAR string
39 | 7	MRNM	Mate Reference sequence NaMe (`=' if same as RNAME)
40 | 8	MPOS	1-based Mate POSistion
41 | 9	TLEN	inferred Template LENgth (insert size)
42 | 10	SEQ	query SEQuence on the same strand as the reference
43 | 11	QUAL	query QUALity (ASCII-33 gives the Phred base quality)
44 | 12+	OPT	variable OPTional fields in the format TAG:VTYPE:VALUE
45 | .TE
46 | .PP
47 | Each bit in the FLAG field is defined as:
48 | .TS
49 | lcbl.
50 | 0x0001	p	the read is paired in sequencing
51 | 0x0002	P	the read is mapped in a proper pair
52 | 0x0004	u	the query sequence itself is unmapped
53 | 0x0008	U	the mate is unmapped
54 | 0x0010	r	strand of the query (1 for reverse)
55 | 0x0020	R	strand of the mate
56 | 0x0040	1	the read is the first read in a pair
57 | 0x0080	2	the read is the second read in a pair
58 | 0x0100	s	the alignment is not primary
59 | 0x0200	f	the read fails platform/vendor quality checks
60 | 0x0400	d	the read is either a PCR or an optical duplicate
61 | 0x0800	S	the alignment is supplementary
62 | .TE
63 | .P
64 | where the second column gives the string representation of the FLAG field.
65 | .SH SEE ALSO
66 | .TP
67 | https://github.com/samtools/hts-specs
68 | The full SAM/BAM file format specification
69 | 


--------------------------------------------------------------------------------
/lib/htslib/test/auxf#values.sam:
--------------------------------------------------------------------------------
1 | @HD	VN:1.4	SO:unsorted
2 | @SQ	SN:Sheila	LN:20
3 | @RG	ID:ID	SM:foo
4 | Fred	16	Sheila	1	86	10M	*	0	0	GCTAGCTCAG	**********	RG:Z:ID	A!:A:!	Ac:A:c	AC:A:C	I0:i:0	I1:i:1	I2:i:127	I3:i:128	I4:i:255	I5:i:256	I6:i:32767	I7:i:32768	I8:i:65535	I9:i:65536	IA:i:2147483647	i1:i:-1	i2:i:-127	i3:i:-128	i4:i:-255	i5:i:-256	i6:i:-32767	i7:i:-32768	i8:i:-65535	i9:i:-65536	iA:i:-2147483647	iB:i:-2147483648	F0:f:-1	F1:f:0	F2:f:1	F3:f:9.9e-19	F4:f:-9.9e-19	F5:f:9.9e+19	F6:f:-9.9e+19	H0:H:AA	H1:H:dead00beef	Z0:Z:space space	Zn:Z:	Hn:H:
5 | Jim	16	Sheila	11	11	10M	*	0	0	AAAAAAAAAA	*	BC:B:C,0,127,128,255	Bc:B:c,-128,-127,0,127	BS:B:S,0,32767,32768,65535	Bs:B:s,-32768,-32767,0,32767	BI:B:I,0,2147483647,2147483648,4294967295	Bi:B:i,-2147483648,-2147483647,0,2147483647	Hn:H:	Zn:Z:
6 | 


--------------------------------------------------------------------------------
/lib/htslib/test/auxf#values_java.cram:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/auxf#values_java.cram


--------------------------------------------------------------------------------
/lib/htslib/test/auxf.fa:
--------------------------------------------------------------------------------
1 | >Sheila
2 | GCTAGCTCAGAAAAAAAAAA
3 | 


--------------------------------------------------------------------------------
/lib/htslib/test/auxf.fa.fai:
--------------------------------------------------------------------------------
1 | Sheila	20	8	20	21
2 | 


--------------------------------------------------------------------------------
/lib/htslib/test/bgziptest.txt:
--------------------------------------------------------------------------------
1 | 122333444455555


--------------------------------------------------------------------------------
/lib/htslib/test/bgziptest.txt.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/bgziptest.txt.gz


--------------------------------------------------------------------------------
/lib/htslib/test/bgziptest.txt.gz.gzi:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/bgziptest.txt.gz.gzi


--------------------------------------------------------------------------------
/lib/htslib/test/c1#bounds.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:c1	LN:10
2 | s0	0	c1	1	0	10M	*	0	0	AACCGCGGTT	**********
3 | s1	0	c1	2	0	10M	*	0	0	ACCGCGGTTC	**********
4 | s2	0	c1	3	0	10M	*	0	0	CCGCGGTTCG	**********
5 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1#clip.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:c1	LN:10
2 | s0a	0	c1	1	0	10M	*	0	0	AACCGCGGTT	**********
3 | s0A	0	c1	1	0	3M4N3M	*	0	0	AACGTT	******
4 | s0b	0	c1	2	0	1S8M1S	*	0	0	AACCGCGGTT	**********
5 | s0B	0	c1	2	0	1H8M1H	*	0	0	ACCGCGGT	********
6 | s0c	0	c1	3	0	2S6M2S	*	0	0	AACCGCGGTT	**********
7 | s0c	0	c1	3	0	2S3M2I3M2S	*	0	0	AACCGNNCGGTT	************
8 | s0C	0	c1	3	0	2H6M2H	*	0	0	CCGCGG	******
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1#noseq.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:c1	LN:10
 2 | sq1	0	c1	1	0	10M	*	0	0	AACCGCGGTT	**********	MD:Z:10	NM:i:0
 3 | sQ1	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*	MD:Z:10	NM:i:0
 4 | SQ1	0	c1	1	0	10M	*	0	0	*	*	MD:Z:10	NM:i:0
 5 | sq2	0	c1	1	0	4M1D5M	*	0	0	AACCCGGTT	*********	MD:Z:4^G5	NM:i:1
 6 | sQ2	0	c1	1	0	4M1D5M	*	0	0	AACCCGGTT	*	MD:Z:4^G5	NM:i:1
 7 | SQ2	0	c1	1	0	4M1D5M	*	0	0	*	*	MD:Z:4^G5	NM:i:1
 8 | sq3	4	c1	1	0	*	*	0	0	AACCCGGTT	*********
 9 | sQ3	4	c1	1	0	*	*	0	0	AACCCGGTT	*
10 | SQ3	4	c1	1	0	*	*	0	0	*	*
11 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1#pad1.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:c1	LN:10
 2 | s0a	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 3 | s0b	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 4 | s0c	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 5 | s1	0	c1	1	0	5M6I5M	*	0	0	AACCGGTTAACCGGTT	*
 6 | s2	0	c1	1	0	5M1P4I1P5M	*	0	0	AACCGTTAACGGTT	*
 7 | s3	0	c1	1	0	5M3I3P5M	*	0	0	AACCGGTTCGGTT	*
 8 | s4	0	c1	1	0	5M3P3I5M	*	0	0	AACCGAACCGGTT	*
 9 | s5	0	c1	1	0	4M1D2P2I2P1D4M	*	0	0	AACCTAGGTT	*
10 | s6	0	c1	1	0	2M3D6I3D2M	*	0	0	AAGTTAACTT	*
11 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1#pad2.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:c1	LN:10
 2 | s0a	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 3 | s0b	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 4 | s0c	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 5 | s0d	0	c1	1	0	10M	*	0	0	AACCGCGGTT	*
 6 | s1	0	c1	1	0	5M6I5M	*	0	0	AACCGGTTAACCGGTT	*
 7 | s2	0	c1	1	0	5M1P4I1P5M	*	0	0	AACCGTTAACGGTT	*
 8 | s3	0	c1	1	0	5M3I3P5M	*	0	0	AACCGGTTCGGTT	*
 9 | s4	0	c1	1	0	5M3P3I5M	*	0	0	AACCGAACCGGTT	*
10 | s5	0	c1	1	0	4M1D2P2I2P1D4M	*	0	0	AACCTAGGTT	*
11 | s6	0	c1	1	0	2M3D6I3D2M	*	0	0	AAGTTAACTT	*
12 | s7	0	c1	1	0	4M2D4M	*	0	0	AACCGGTT	*
13 | s8	0	c1	1	0	5D2P2I2P5D	*	0	0	TA	*
14 | s9	0	c1	5	0	1M2P2I2P	*	0	0	GTA	*
15 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1#pad3.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:c1	LN:10
 2 | @RG	ID:p.sam	SM:unknown	LB:p.sam
 3 | s0a	0	c1	6	0	5I6P5M	*	0	0	AACCGCGGTT	*	RG:Z:p.sam
 4 | s0b	0	c1	6	0	5I6P5M	*	0	0	AACCGCGGTT	*	RG:Z:p.sam
 5 | s0c	0	c1	6	0	5I6P5M	*	0	0	AACCGCGGTT	*	RG:Z:p.sam
 6 | s0d	0	c1	6	0	5I6P5M	*	0	0	AACCGCGGTT	*	RG:Z:p.sam
 7 | s1	0	c1	6	0	11I5M	*	0	0	AACCGGTTAACCGGTT	*	RG:Z:p.sam
 8 | s2	0	c1	6	0	5I1P4I1P5M	*	0	0	AACCGTTAACGGTT	*	RG:Z:p.sam
 9 | s3	0	c1	6	0	8I3P5M	*	0	0	AACCGGTTCGGTT	*	RG:Z:p.sam
10 | s4	0	c1	6	0	5I3P3I5M	*	0	0	AACCGAACCGGTT	*	RG:Z:p.sam
11 | s5	0	c1	6	0	4I3P2I2P1D4M	*	0	0	AACCTAGGTT	*	RG:Z:p.sam
12 | s6	0	c1	6	0	2I3P6I3D2M	*	0	0	AAGTTAACTT	*	RG:Z:p.sam
13 | s7	0	c1	6	0	4I7P1D4M	*	0	0	AACCGGTT	*	RG:Z:p.sam
14 | s8	0	c1	6	0	7P2I2P	*	0	0	TA	!!	RG:Z:p.sam
15 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1#unknown.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:c1	LN:10
 2 | @CO	Tests permuations of seq / qual being present or "*" in mapped
 3 | @CO	and unmapped forms.  Also tests MD/NM tag generation.
 4 | _sqm	0	c1	1	0	2M1I4M1D3M	*	0	0	AACCCTCGTT	IIIIIIIIII	MD:Z:4G1^G3	NM:i:3
 5 | _sm	0	c1	1	0	2M1I4M1D3M	*	0	0	AACCCTCGTT	*	MD:Z:4G1^G3	NM:i:3
 6 | _m	0	c1	1	0	2M1I4M1D3M	*	0	0	*	*	MD:Z:4G1^G3	NM:i:3
 7 | _squ	4	c1	1	0	*	*	0	0	AACCCTCGTT	IIIIIIIIII
 8 | _su	4	c1	1	0	*	*	0	0	AACCCTCGTT	*
 9 | _u	4	c1	1	0	*	*	0	0	*	*
10 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1.fa:
--------------------------------------------------------------------------------
1 | >c1
2 | AACCGCGGTT
3 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c1.fa.fai:
--------------------------------------------------------------------------------
1 | c1	10	4	10	11
2 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c2#pad.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:c2	LN:9
 2 | @CO
 3 | @CO	mpileup example from https://github.com/samtools/htslib/issues/59
 4 | @CO	with additional Pad cigar operations
 5 | @CO
 6 | @CO	 c2    CC***AA**T**AA***CC
 7 | @CO
 8 | @CO	+s1    CT***AA**T**AA***TC
 9 | @CO	+s1b   CT*******T*******TC
10 | @CO	+s2    CT*****G***G*****TC
11 | @CO	+s2p   CT*****G***G*****TC
12 | @CO	+s3    CT*****GG*GG*****TC
13 | @CO	+s3b   CT****CGGCGGC****TC
14 | @CO	+s4    CT***AAG***GAA***TC
15 | @CO	+s4p   CT***AAG***GAA***TC
16 | @CO	+s5    CTGGG*********GGGTC
17 | @CO
18 | s1	0	c2	1	0	9M	*	0	0	CTAATAATC	XXXXXXXXX
19 | s1b	0	c2	1	0	2M2D1M2D2M	*	0	0	CTTTC	*
20 | s2	0	c2	1	0	2M2D1I1D1I2D2M	*	0	0	CTGGTC	*
21 | s2p	0	c2	1	0	2M2D1I1P1D1P1I2D2M	*	0	0	CTGGTC	*
22 | s3	0	c2	1	0	2M2D2I1D2I2D2M	*	0	0	CTGGGGTC	*
23 | s3b	0	c2	1	0	2M1D1M2I1M2I1M1D2M	*	0	0	CTCGGCGGCTC	*
24 | s4	0	c2	1	0	4M1I1D1I4M	*	0	0	CTAAGGAATC	*
25 | s4p	0	c2	1	0	4M1I1P1D1P1I4M	*	0	0	CTAAGGAATC	*
26 | s5	0	c2	1	0	2M3I5D3I2M	*	0	0	CTGGGGGGTC	*
27 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c2.fa:
--------------------------------------------------------------------------------
1 | >c2
2 | CCAATAACC
3 | 


--------------------------------------------------------------------------------
/lib/htslib/test/c2.fa.fai:
--------------------------------------------------------------------------------
1 | c2	9	4	9	10
2 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#1.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:CHROMOSOME_I	LN:1009800
2 | SRR065390.14978392	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	AS:i:-18	XS:i:-18	YT:Z:UU
3 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#2.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:CHROMOSOME_I	LN:1009800
2 | SRR065390.14978392	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
3 | SRR065390.921023	16	CHROMOSOME_I	3	12	100M	*	0	0	CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000	XG:i:0	XM:i:3	XN:i:0	XO:i:0	AS:i:-6	XS:i:-13	YT:Z:UU
4 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#5.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:CHROMOSOME_I	LN:1009800
 2 | @SQ	SN:CHROMOSOME_II	LN:5000
 3 | @SQ	SN:CHROMOSOME_III	LN:5000
 4 | @SQ	SN:CHROMOSOME_IV	LN:5000
 5 | @SQ	SN:CHROMOSOME_V	LN:5000
 6 | I	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
 7 | II.14978392	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
 8 | III	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
 9 | IV	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
10 | V	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
11 | VI	2048	CHROMOSOME_I	2	1	27M100000D73M	*	0	0	ACTAAGCCTAAGCCTAAGCCTAAGCCAATTATCGATTTCTGAAAAAATTATCGAATTTTCTAGAAATTTTGCAAATTTTTTCATAAAATTATCGATTTTA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#5b.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:CHROMOSOME_I	LN:1009800
 2 | @SQ	SN:CHROMOSOME_II	LN:5000
 3 | @SQ	SN:CHROMOSOME_III	LN:5000
 4 | @SQ	SN:CHROMOSOME_IV	LN:5000
 5 | @SQ	SN:CHROMOSOME_V	LN:5000
 6 | I	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
 7 | II.14978392	16	CHROMOSOME_II	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
 8 | III	16	CHROMOSOME_III	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
 9 | IV	16	CHROMOSOME_IV	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
10 | V	16	CHROMOSOME_V	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	XG:i:1	XM:i:5	XN:i:0	XO:i:1	XS:i:-18	AS:i:-18	YT:Z:UU
11 | VI	0	CHROMOSOME_V	10	1	7S20M1D23M10I30M10S	*	0	0	AGCCTAAGCCTAAGCCTAAGCCTAAGCTAAGCCTAAGCCTAAGCCTAAGCTTTTTTTTTTCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	*
12 | VI	256	CHROMOSOME_V	10	1	7S20M1D23M10I30M10S	*	0	0	*	*
13 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#5b_java.cram:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/ce#5b_java.cram


--------------------------------------------------------------------------------
/lib/htslib/test/ce#supp.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:CHROMOSOME_I	LN:1009800
2 | @CO	Test supplementary reads, for CRAM
3 | supp	99	CHROMOSOME_I	100	1	50M50S	*	0	0	TAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTACCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCC	*
4 | supp	2147	CHROMOSOME_I	200	1	50H50M	*	0	0	CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCC	*
5 | supp	2195	CHROMOSOME_I	500	1	50M50H	*	0	0	TTTTAGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCC	*
6 | supp	147	CHROMOSOME_I	600	1	50S50M	*	0	0	TTTTAGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAG	*
7 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#tag_depadded.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.4	SO:coordinate
 2 | @RG	ID:UNKNOWN	SM:unknown	LB:UNKNOWN
 3 | @SQ	SN:CHROMOSOME_I	LN:1009800
 4 | I	16	CHROMOSOME_I	2	1	100M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	PT:Z:27;28;+;STOP;Note=tag1
 5 | II.14978392	16	CHROMOSOME_I	2	1	100M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	PT:Z:27;27;+;PRIM;Note=tag2|28;28;+;OLIG;Note=tag3
 6 | III	0	CHROMOSOME_I	2	1	27M1I73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTCAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	###########################"##@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	PT:Z:1;1;+;COMM|101;101;+;COMM
 7 | IV	16	CHROMOSOME_I	2	1	100M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
 8 | V	0	CHROMOSOME_I	2	1	100M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
 9 | *	768	CHROMOSOME_I	2	255	1M	*	0	0	*	*	CT:Z:+;STOP
10 | *	768	CHROMOSOME_I	28	255	2M	*	0	0	*	*	CT:Z:+;COMM;Note=consensus%0Amulti%09line%0Atag%0A!"#$%25^&*()_+<>?:@~{}%7C%0A1234567890-=[]'%3B#,./\
11 | *	768	CHROMOSOME_I	101	255	1M	*	0	0	*	*	CT:Z:+;STOP
12 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#tag_padded.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.4	SO:coordinate
 2 | @RG	ID:UNKNOWN	SM:unknown	LB:UNKNOWN
 3 | @SQ	SN:CHROMOSOME_I	LN:1009800
 4 | I	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	PT:Z:27;29;+;STOP;Note=tag1
 5 | II.14978392	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	PT:Z:27;27;+;PRIM;Note=tag2|29;29;+;OLIG;Note=tag3
 6 | III	0	CHROMOSOME_I	2	1	101M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTCAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	###########################"##@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	PT:Z:1;1;+;COMM|101;101;+;COMM
 7 | IV	16	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
 8 | V	0	CHROMOSOME_I	2	1	27M1D73M	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
 9 | *	768	CHROMOSOME_I	2	255	1M	*	0	0	*	*	CT:Z:+;STOP
10 | *	768	CHROMOSOME_I	28	255	3M	*	0	0	*	*	CT:Z:+;COMM;Note=consensus%0Amulti%09line%0Atag%0A!"#$%25^&*()_+<>?:@~{}%7C%0A1234567890-=[]'%3B#,./\
11 | *	768	CHROMOSOME_I	102	255	1M	*	0	0	*	*	CT:Z:+;STOP
12 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#unmap.sam:
--------------------------------------------------------------------------------
1 | I	4	*	0	1	*	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2 | II	4	*	0	1	*	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3 | III	4	*	0	1	*	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
4 | IV	4	*	0	1	*	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5 | V	4	*	0	1	*	*	0	0	CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6 | VI	4	*	0	1	*	*	0	0	ACTAAGCCTAAGCCTAAGCCTAAGCCAATTATCGATTTCTGAAAAAATTATCGAATTTTCTAGAAATTTTGCAAATTTTTTCATAAAATTATCGATTTTA	#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce#unmap1.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.0	SO:unsorted
 2 | @SQ	SN:CHROMOSOME_I	LN:1009800
 3 | @SQ	SN:CHROMOSOME_II	LN:5000
 4 | @SQ	SN:CHROMOSOME_III	LN:5000
 5 | @SQ	SN:CHROMOSOME_IV	LN:5000
 6 | @SQ	SN:CHROMOSOME_V	LN:5000
 7 | @SQ	SN:CHROMOSOME_X	LN:5000
 8 | @SQ	SN:CHROMOSOME_MtDNA	LN:5000
 9 | @RG	ID:UNKNOWN	SM:UNKNOWN
10 | @PG	ID:bowtie2	PN:bowtie2	VN:2.0.0-beta5
11 | SRR065390.33808391	4	*	0	0	*	*	0	0	GATCGCACTGAAAATCTGGATATAGAACGTGTGCAAATGATTGTCTCTACCGTTCCGTAAAAATTATTGCTAATTAGCAATGATTTTAAGCTAATTAGTT	CCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCB;CCCAACCCCCCCCCCCCCD=B9BCABCBCB>BBBC@B<<@BA;BCC?B>A<<@(?:4==4	YT:Z:UU
12 | SRR065390.33808433	4	*	0	0	*	*	0	0	NCATCTTCTGCAGGCGCGGTCGGCACCGTGTATTCGTTACGTTCCACGCCGATGATATTAGACACCAGCACGGTGTGATGCGCAGTCACCGCACGACCCG	!###################################################################################################	YT:Z:UU
13 | SRR065390.33808462	4	*	0	0	*	*	0	0	NGTTTGAGCGCAATGACTTGACGATGACCGGTGATTACAGTAACCAGCATATTGTGCCGATGAAGCAGGCTGTCGCTCCGCAATTTGAAGAGGGACACGA	!###################################################################################################	YT:Z:UU
14 | SRR065390.33808468	4	*	0	0	*	*	0	0	NGCTTCCCACTATATTTTACTCTCTGTGGCTTCCCACTTTATTTTACTCTCTGTGGCTTTATCGATTATTTTTTTCTCCTTGGCTTTCCTCTTTATTTTT	!))))))''&585555AAAAA6AA############################################################################	YT:Z:UU
15 | SRR065390.33808471	4	*	0	0	*	*	0	0	NCGTCTTCTGCGGTTTCTATGATAGAGCAATTCTGTGGCGGATATTAAGATAACGGGTATCTGTTCTTTAATGATGCCGCAAAAAATGGAAAGTTAAGAA	!###################################################################################################	YT:Z:UU
16 | SRR065390.33808489	4	*	0	0	*	*	0	0	NGGAAATTCTGCGGTATCGAGAGATATTTGCCTTTAATTACCCCATAGCCGATTAACATCCCGGCACTATTAATCATTTCAATATTATCAATCACAAAGT	!###################################################################################################	YT:Z:UU
17 | SRR065390.33808504	4	*	0	0	*	*	0	0	NTGGAACACCATGCCCACTTTCGCACGCAGCAGGGCGATATCCTGAGAGTTGGTCAGGATGTTGTCGCCATCAAGCAGAATTTCACCTTCCGCACGCTGC	!###################################################################################################	YT:Z:UU
18 | SRR065390.33808511	4	*	0	0	*	*	0	0	NCAGAAATATATTGAACTTTTGAAACATGTCCCAACTTTTTTTTTTTTTAGAACACGTTGGCTGGTTTTTCAAGTTTTGAATACTTTTTAGGTTTTTTTG	!***()(+++AAAAAAAAAA:78:8318::AAAAAAAAAAAA##########################################################	YT:Z:UU
19 | SRR065390.33808521	4	*	0	0	*	*	0	0	NTGTCAATACATTGTAAGGATTTCCCATTATGTCAATACATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATTTCGTATGTCGTGTTTCTTT	!###################################################################################################	YT:Z:UU
20 | SRR065390.33808523	4	*	0	0	*	*	0	0	NTACTTCTTACAAGATTTTTATCGCTACTTGAAAAAAATTCATCAACATAATCGCCATGACTATCTGCACCGTGAGTATGATAAGCAGCAACTCTATCTG	!***+--,')AAAA778577A72AA50888AAAAAAA72A88858AAAA77AAAAAA7AAAAAAAAA8AA##############################	YT:Z:UU
21 | 


--------------------------------------------------------------------------------
/lib/htslib/test/ce.fa.fai:
--------------------------------------------------------------------------------
1 | CHROMOSOME_I	1009800	14	50	51
2 | CHROMOSOME_II	5000	1030025	50	51
3 | CHROMOSOME_III	5000	1035141	50	51
4 | CHROMOSOME_IV	5000	1040256	50	51
5 | CHROMOSOME_V	5000	1045370	50	51
6 | CHROMOSOME_X	5000	1050484	50	51
7 | CHROMOSOME_MtDNA	5000	1055602	50	51
8 | 


--------------------------------------------------------------------------------
/lib/htslib/test/faidx.fa:
--------------------------------------------------------------------------------
 1 | >
 2 | ATGC
 3 | >trailingblank1
 4 | AAATTTGGGCCC
 5 | TTTGGGCCCAAA
 6 | GGGCCCAAA
 7 | 
 8 | >trailingblank2 with last dna line the same length
 9 | AAATTTGGGCCCAAATTTGGGCCC
10 | TTTGGGCCCAAATTTGGGCCCAAA
11 | GGGCCCAAATTTGGGCCCAAATTT
12 | 
13 | >trailingblank3 with cr-lf style line endings
14 | ACGT
15 | A
16 | 
17 | >  foo
18 | TGCATG
19 | CA
20 | > bar description
21 | TTTTAAAA
22 | 


--------------------------------------------------------------------------------
/lib/htslib/test/fieldarith.c:
--------------------------------------------------------------------------------
 1 | /*  test/fieldarith.c -- CIGAR field arithmetic test suite.
 2 | 
 3 |     Copyright (C) 2013 Genome Research Ltd.
 4 | 
 5 |     Author: John Marshall <jm18@sanger.ac.uk>
 6 | 
 7 | Permission is hereby granted, free of charge, to any person obtaining a copy
 8 | of this software and associated documentation files (the "Software"), to deal
 9 | in the Software without restriction, including without limitation the rights
10 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 | copies of the Software, and to permit persons to whom the Software is
12 | furnished to do so, subject to the following conditions:
13 | 
14 | The above copyright notice and this permission notice shall be included in
15 | all copies or substantial portions of the Software.
16 | 
17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 | DEALINGS IN THE SOFTWARE.  */
24 | 
25 | #include <config.h>
26 | 
27 | #include <stdio.h>
28 | 
29 | #include "htslib/sam.h"
30 | 
31 | int ntests = 0;
32 | int nfailures = 0;
33 | 
34 | void check(const bam1_t *aln, const char *testname, const char *tag, int value)
35 | {
36 |     int32_t refvalue;
37 |     uint8_t *aux = bam_aux_get(aln, tag);
38 |     if (!aux) return;
39 |     ntests++;
40 |     refvalue = bam_aux2i(aux);
41 |     if (value != refvalue) {
42 |         fprintf(stderr, "%s FAIL for %s: computed %d != %d expected\n",
43 |                 testname, bam_get_qname(aln), value, refvalue);
44 |         nfailures++;
45 |     }
46 | }
47 | 
48 | int main(int argc, char **argv)
49 | {
50 |     bam_hdr_t *header;
51 |     bam1_t *aln = bam_init1();
52 |     int i;
53 | 
54 |     for (i = 1; i < argc; i++) {
55 |         samFile *in = sam_open(argv[i], "r");
56 |         if (in == NULL) { perror(argv[1]); return 1; }
57 | 
58 |         header = sam_hdr_read(in);
59 |         while (sam_read1(in, header, aln) >= 0) {
60 |             check(aln, "cigar2qlen", "XQ",
61 |                   bam_cigar2qlen(aln->core.n_cigar, bam_get_cigar(aln)));
62 |             check(aln, "cigar2rlen", "XR",
63 |                   bam_cigar2rlen(aln->core.n_cigar, bam_get_cigar(aln)));
64 |             check(aln, "endpos", "XE", bam_endpos(aln));
65 |         }
66 | 
67 |         bam_hdr_destroy(header);
68 |         sam_close(in);
69 |     }
70 | 
71 |     bam_destroy1(aln);
72 | 
73 |     return (nfailures > 0);
74 | }
75 | 


--------------------------------------------------------------------------------
/lib/htslib/test/fieldarith.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:one	LN:1000
 2 | @SQ	SN:two	LN:500
 3 | @CO	For each SAM record that has each listed aux field, performs these tests:
 4 | @CO	XQ is the expected result for bam_cigar2qlen()
 5 | @CO	XR is the expected result for bam_cigar2rlen()
 6 | @CO	XE is the expected result for bam_endpos()
 7 | @CO	(Note that these are all zero-based, while POS is one-based in SAM)
 8 | r1	0	one	50	20	8M	*	0	0	ATGCATGC	qqqqqqqq	XQ:i:8	XR:i:8	XE:i:57
 9 | r2	0	one	100	20	50M	*	0	0	ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT	qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq	XQ:i:50	XR:i:50	XE:i:149
10 | unmapped	5	two	200	0	*	two	200	0	ATGCATGC	qqqqqqqq	XQ:i:0	XR:i:0	XE:i:200
11 | hascigar	5	two	200	0	6M2S	two	200	0	ATGCATGC	qqqqqqqq	XQ:i:8	XR:i:6	XE:i:200
12 | s1	0	one	300	20	2M	*	0	0	AT	qq	XQ:i:2	XR:i:2	XE:i:301
13 | su1	4	*	0	0	*	*	0	0	AT	qq	XQ:i:0	XR:i:0	XE:i:0
14 | su2	5	two	400	0	*	two	400	0	AT	qq	XQ:i:0	XR:i:0	XE:i:400
15 | su3	4	one	500	0	2M	*	0	0	AT	qq	XQ:i:2	XR:i:2	XE:i:500
16 | 


--------------------------------------------------------------------------------
/lib/htslib/test/formatcols.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.3
2 | ##FILTER=<ID=PASS,Description="All filters passed">
3 | ##contig=<ID=1>
4 | ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
5 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
6 | 1	100	a	A	T	.	.	.	S	a	bbbbbbb	ccccccccc
7 | 


--------------------------------------------------------------------------------
/lib/htslib/test/formatmissing-out.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.3
2 | ##FILTER=<ID=PASS,Description="All filters passed">
3 | ##contig=<ID=1>
4 | ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
5 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
6 | 1	100	a	A	T	.	.	.	.	.	.	.
7 | 


--------------------------------------------------------------------------------
/lib/htslib/test/formatmissing.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.3
2 | ##FILTER=<ID=PASS,Description="All filters passed">
3 | ##contig=<ID=1>
4 | ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
5 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
6 | 1	100	a	A	T	.	.	.	.	.	.	.
7 | 


--------------------------------------------------------------------------------
/lib/htslib/test/md#1.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.0	SO:coordinate
 2 | @SQ	SN:a	LN:40
 3 | x	0	a	1	255	40M	*	0	0	AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT	*	NM:i:2	MD:Z:19N0N19
 4 | x*	0	a	1	255	40M	*	0	0	CAAAAAAAANNCCCCCCCYNNRGGGGGGGGTTTTTTTTTC	*	NM:i:6	MD:Z:0A8A0C8N0N18T0
 5 | xIP	0	a	1	255	1I10M1I10M2I10M2P3I2P10M1I	*	0	0	NAAAAAAAAAAGCCCCCCCCCCAAGGGGGGGGGGCCCTTTTTTTTTTN	*	NM:i:12	MD:Z:18Y0N0N0R18
 6 | xIP*	0	a	1	255	1I10M1I10M2I10M2P3I2P10M1I	*	0	0	NCAAAAAAAAAGCCCCCCCCCCAAGGGGGGGGGACCCATTTTTTTTCN	*	NM:i:16	MD:Z:0A17Y0N0N0R7G0T8T0
 7 | xD	0	a	1	255	9M1D8M2D7M3D6M	*	0	0	AAAAAAAAACCCCCCYNNRGGGGGTTTTTT	*	NM:i:9	MD:Z:9^A6C0C0^YN0N6^GGG6
 8 | xD*	0	a	1	255	9M1D8M2D7M3D6M	*	0	0	CAAAAAAANNCCCCCCTTGGGGGGTTTTTA	*	NM:i:13	MD:Z:0A7A0^A0C6C0^YN0N0R5^GGG5T0
 9 | xN	0	a	1	255	10M20N10M	*	0	0	AAAAAAAAAATTTTTTTTTT	*	NM:i:0	MD:Z:20
10 | xN*	0	a	1	255	10M20N10M	*	0	0	CAAAAAAACCAATTTTTTTA	*	NM:i:6	MD:Z:0A7A0A0T0T7T0
11 | xS	0	a	11	255	5H10S20M10S5H	*	0	0	AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT	*	NM:i:2	MD:Z:9N0N9
12 | xS*	0	a	11	255	5H10S20M10S5H	*	0	0	CAAAATAAAACCCCCCCCYNNRGGGGGGGGTTTTATTTTC	*	NM:i:2	MD:Z:9N0N9
13 | 


--------------------------------------------------------------------------------
/lib/htslib/test/md.fa:
--------------------------------------------------------------------------------
1 | >a
2 | AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT
3 | 
4 | 


--------------------------------------------------------------------------------
/lib/htslib/test/md.fa.fai:
--------------------------------------------------------------------------------
1 | a	40	3	40	41
2 | 


--------------------------------------------------------------------------------
/lib/htslib/test/noroundtrip-out.vcf:
--------------------------------------------------------------------------------
 1 | ##fileformat=VCFv4.3
 2 | ##FILTER=<ID=PASS,Description="All filters passed">
 3 | ##contig=<ID=3>
 4 | ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 5 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
 6 | 3	50	.	A	T	0	PASS	.	GT:GT	2,4:.
 7 | 3	60	.	T	C	0	PASS	.	GT	0/1
 8 | 3	70	.	G	A	0	PASS	.	GT:GT	2,4:.
 9 | 3	80	.	C	G	0	PASS	.	GT:GT	2,4:0/1
10 | 


--------------------------------------------------------------------------------
/lib/htslib/test/noroundtrip.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.3
2 | ##contig=<ID=3>
3 | ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
4 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
5 | 3	50	.	A	T	0	PASS	.	GT:GT	0/1
6 | 3	60	.	T	C	0	PASS	.	GT	0/1
7 | 3	70	.	G	A	0	PASS	.	GT:GT	0/1:.
8 | 3	80	.	C	G	0	PASS	.	GT:GT	0/1:0/1
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/range.bam:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/range.bam


--------------------------------------------------------------------------------
/lib/htslib/test/range.bam.bai:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/range.bam.bai


--------------------------------------------------------------------------------
/lib/htslib/test/range.cram:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/range.cram


--------------------------------------------------------------------------------
/lib/htslib/test/range.cram.crai:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/range.cram.crai


--------------------------------------------------------------------------------
/lib/htslib/test/realn01.fa:
--------------------------------------------------------------------------------
 1 | >000000F 57093-57778
 2 | CAGACAAACATACACCATCAGACAGCAGCACCATATTCTTTTTTTCTGCTAATTTGCTAA
 3 | TTACACAAACACAGACACTAAGAAATATTCTTCCCCTTTGGAAAATGTTTTCCACATTGA
 4 | ATCATGGTTGATTTCATTCATATTTTTTACGCTAATTAAAAAAATAAAGACTCTTTCATG
 5 | TGAAAACAGAGCTTCACAAAGTACTCTCATTCTCACCGCTAGCAGGCTGACAATCAGCAG
 6 | CAGACAGAGCATGATGTGTCTGATGGTCTGGTTGTCATCTGTCTGGGATTGAAGGCCAGG
 7 | TGGCGGCAGATCTAATGGCTGCTCAGGAGGCAGAAGAACTCTGTTGCTGCCCATCACACA
 8 | GCGCCCCACTGTGGTCTGAAGTAAAAAAGTTCATGTACTCGCATGAGAGTTATGTGTAAA
 9 | ACAGAGCTCAATTTTATTTTGTATTTATTGTGCAGTTAGAAAATAATATGATCAAATCTG
10 | TTTGTTTACCTGTGTTGTTTGTGTGCTCCCTCTGCGTGCTGGCTATCATGTCAGGTACTG
11 | GTCTGGACCGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAG
12 | TTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAT
13 | ACAAATTACATCTAGATATTTGTTAT
14 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn01.fa.fai:
--------------------------------------------------------------------------------
1 | 000000F	686	21	60	61
2 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn01.sam:
--------------------------------------------------------------------------------
1 | @HD	VN:1.4	SO:coordinate
2 | @SQ	SN:000000F	LN:686
3 | @RG	ID:rg	SM:sample
4 | @CO	The alignment on the first read overhangs the reference by two bases
5 | ST-E00128:308:HHVVLALXX:8:1217:16001:6565	147	000000F	532	60	6M1D117M5D28M	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	MD:Z:6^C10C106^ACAAT28	PG:Z:MarkDuplicates	NM:i:7	AS:i:129	XS:i:20	RG:Z:rg
6 | ST-E00128:308:HHVVLALXX:8:1217:16001:6566	147	000000F	532	60	6M1D117M5D26M2S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
7 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151I	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
8 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn01_exp-a.sam:
--------------------------------------------------------------------------------
1 | @HD	VN:1.4	SO:coordinate
2 | @SQ	SN:000000F	LN:686
3 | @RG	ID:rg	SM:sample
4 | @CO	The alignment on the first read overhangs the reference by two bases
5 | ST-E00128:308:HHVVLALXX:8:1217:16001:6565	147	000000F	532	60	6M1D117M5D28M	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJ96!!%(6JJJJJJJJJJJJJJJJJD@>$!!	MD:Z:6^C10C106^ACAAT28	PG:Z:MarkDuplicates	NM:i:7	AS:i:129	XS:i:20	RG:Z:rg	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QTieabT@@@@@@@@@@@@@@@@@FFHb``
6 | ST-E00128:308:HHVVLALXX:8:1217:16001:6566	147	000000F	532	60	6M1D117M5D26M2S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJ96!!%(6JJJJJJJJJJJJJJJJJD@>$AA	PG:Z:MarkDuplicates	RG:Z:rg	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QTieabT@@@@@@@@@@@@@@@@@FFHb@@
7 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151I	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
8 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn01_exp-e.sam:
--------------------------------------------------------------------------------
1 | @HD	VN:1.4	SO:coordinate
2 | @SQ	SN:000000F	LN:686
3 | @RG	ID:rg	SM:sample
4 | @CO	The alignment on the first read overhangs the reference by two bases
5 | ST-E00128:308:HHVVLALXX:8:1217:16001:6565	147	000000F	532	60	6M1D117M5D28M	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	MD:Z:6^C10C106^ACAAT28	PG:Z:MarkDuplicates	NM:i:7	AS:i:129	XS:i:20	RG:Z:rg	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QTieabT@@@@@@@@@@@@@@@@@FFHb``
6 | ST-E00128:308:HHVVLALXX:8:1217:16001:6566	147	000000F	532	60	6M1D117M5D26M2S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QTieabT@@@@@@@@@@@@@@@@@FFHb@@
7 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151I	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
8 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn01_exp.sam:
--------------------------------------------------------------------------------
1 | @HD	VN:1.4	SO:coordinate
2 | @SQ	SN:000000F	LN:686
3 | @RG	ID:rg	SM:sample
4 | @CO	The alignment on the first read overhangs the reference by two bases
5 | ST-E00128:308:HHVVLALXX:8:1217:16001:6565	147	000000F	532	60	6M1D117M5D28M	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	MD:Z:6^C10C106^ACAAT28	PG:Z:MarkDuplicates	NM:i:7	AS:i:129	XS:i:20	RG:Z:rg	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QTieabT@@@@@@@@@@@@@@@@@FFHb``
6 | ST-E00128:308:HHVVLALXX:8:1217:16001:6566	147	000000F	532	60	6M1D117M5D26M2S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@QTieabT@@@@@@@@@@@@@@@@@FFHb@@
7 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151I	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
8 | ST-E00128:308:HHVVLALXX:8:1217:16001:6567	147	000000F	532	60	151S	=	195	-494	CAGGTATGGTCTGGACAGGAGAGAAACTGTGGATGTCTGTCAACACAACAGAAAAAGTGACTGATTAGTTAGATGTAACTAATTTCAACTATCTAGTCTTCCTCTAAAGACCCCTACTTTAACACAAATTACATCTAGATATTTGTTATTT	7AFAAF<)7<<7<7FA<FFFAF<JFFJFJJJJJAJFFFJAFJFJJJJJJJJJJJFJFFAFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJJFJJFJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJFFFAA	PG:Z:MarkDuplicates	RG:Z:rg
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn02-r.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.0	SO:coordinate
 2 | @SQ	SN:17	LN:4200	SP:Human
 3 | @RG	ID:rg	SM:sample
 4 | ERR013140.3521432	99	17	1	29	22S86M	=	226	313	AGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCA	@AEDGBHIIIIIFJGIKHGHIJJJEJKHJKJKGKLLIFHKLLCJJIDEFFHKHEHHJIIIDJEEEJEIKGJIHCGKHFKFE9BBDIAJAHF4?DE@I:DD48(86D=>	MD:Z:86	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
 5 | ERR156632.12704932	163	17	1	29	36S64M	=	195	293	TGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTG	BFAFGFEIGFEFHHEIDKJGHHHJIIE=@KKGGKJGIBLLMFKMDIIHJKKHFELLLKFIHMHIHHIHLKJFCHFJIJAID=JHKFGHJIHKKCH:@HD?	MD:Z:64	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
 6 | ERR156632.9601178	99	17	1	29	62S38M	=	279	377	CTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGA	DEEEIIHHKIJILKHLHIKEKHHMKLKKJGKKKKLKLFIHEKIKL=KLJLKIILHKMH9LJJJJLHLHJJKJJKMLKJD>MJKLEHIGHIH=FFCHF>BE	MD:Z:38	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
 7 | ERR162872.21706338	99	17	1	29	10S90M	=	246	344	CTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCA	BHBFH<EIFGGGJFEGJJJI?JJKLDGAHJKJIIILHFCJIAKKEJKIJHBIHJBJKDJHKMKJGJLKHIGJ8IGHKL=JGF8KCHKK:HAD4IIDFFFB	MD:Z:90	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
 8 | ERR013140.13475139	99	17	2401	60	88M20S	=	2680	386	AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGCGTTTGAGGCTGCTGT	@CEBEEIHHHICFJIFKGHIKJHII>DBC:CE>A8C>C>7DBA=BEDDB4=9;:<C><??>@=;@D@@=B@E.3?972<>6@8=>?1$0:95%5%*1=8;0%4<228%	X0:i:1	X1:i:0	XC:i:88	MD:Z:88	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
 9 | ERR162875.26247502	83	17	2858	60	100M	=	2581	-376	ACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGAC	<DEHIIBHFHEKJKHBIMJLIHJIKIKKGIMH@LGJIHM=MDJILDKJKMMIJGHLLCLCJ;KKILKHHHKLICJKIHIIIIDDGJFCIHHGHF@EEFFA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
10 | ERR156632.1508798	83	17	3006	29	1S4M1D95M	=	2587	-518	CCCCAAGCAGCAGCCGGGGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTCCCCAGATGCCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCT	<'&*(-+/?*88'-%%(((+KB/N.G)9.5E39>/;,F</*?*3K20GK703/('0'1G9)/,'2KIL6A8.G?I8LFC@>BHLI?CKH=BJ?FEE==DA	MD:Z:4^C6C0A2T1T36G8G36	RG:Z:rg	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
11 | ERR243091.881299	83	17	3491	60	100M	=	3174	-416	CTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAA	C5;=CAAEFDFEEEEBCI;JFIKHGHGHIIKGEKGJIGGIJG=GDIKGFIHIJEIHJFFFFDDDAI>IDJDFGFEIFGHGIFGFJFIDFGEHGGDB@A@?	X0:i:1	X1:i:0	MD:Z:96G3	RG:Z:rg	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
12 | ERR013140.23480670	133	17	3771	0	35M73S	=	3771	0	TTCTCATCAATCCCTCATCTCTTATAACCATTTCGGTCCTTTCGGCCCTACAGCCACCTTGTTTATACTTGGTAAGACCCACACCACTCGCCAACTTACTCTACTCCC	8+7?5>09:),/%81,$,7<+?)+1+*+),3%5+)#%(4B%$&'%'/*@,)*%%&,%(/0%-&$$*$-,$3*.%/$:%$+.$*%&+.,.%%,%(%7(-.-',1*6%&$	XC:i:35	RG:Z:rg
13 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn02.fa.fai:
--------------------------------------------------------------------------------
1 | 17	4200	14	60	61
2 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn02.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.0	SO:coordinate
 2 | @SQ	SN:17	LN:4200	SP:Human
 3 | @RG	ID:rg	SM:sample
 4 | ERR013140.3521432	99	17	1	29	22S86M	=	226	313	AGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCA	@AEDGBHIIIIIFJGIKHGHIJJJEJKHJKJKGKLLIFHKLLCJJIDEFFHKHEHHJIIIDJEEEJEIKGJIHCGKHFKFE9BBDIAJAHF4?DE@I:DD48(86D=>	MD:Z:86	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M
 5 | ERR156632.12704932	163	17	1	29	36S64M	=	195	293	TGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTG	BFAFGFEIGFEFHHEIDKJGHHHJIIE=@KKGGKJGIBLLMFKMDIIHJKKHFELLLKFIHMHIHHIHLKJFCHFJIJAID=JHKFGHJIHKKCH:@HD?	MD:Z:64	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M
 6 | ERR156632.9601178	99	17	1	29	62S38M	=	279	377	CTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGA	DEEEIIHHKIJILKHLHIKEKHHMKLKKJGKKKKLKLFIHEKIKL=KLJLKIILHKMH9LJJJJLHLHJJKJJKMLKJD>MJKLEHIGHIH=FFCHF>BE	MD:Z:38	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M
 7 | ERR162872.21706338	99	17	1	29	10S90M	=	246	344	CTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCA	BHBFH<EIFGGGJFEGJJJI?JJKLDGAHJKJIIILHFCJIAKKEJKIJHBIHJBJKDJHKMKJGJLKHIGJ8IGHKL=JGF8KCHKK:HAD4IIDFFFB	MD:Z:90	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M
 8 | ERR013140.13475139	99	17	2401	60	88M20S	=	2680	386	AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGCGTTTGAGGCTGCTGT	@CEBEEIHHHICFJIFKGHIKJHII>DBC:CE>A8C>C>7DBA=BEDDB4=9;:<C><??>@=;@D@@=B@E.3?972<>6@8=>?1$0:95%5%*1=8;0%4<228%	X0:i:1	X1:i:0	XC:i:88	MD:Z:88	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U
 9 | ERR162875.26247502	83	17	2858	60	100M	=	2581	-376	ACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGAC	<DEHIIBHFHEKJKHBIMJLIHJIKIKKGIMH@LGJIHM=MDJILDKJKMMIJGHLLCLCJ;KKILKHHHKLICJKIHIIIIDDGJFCIHHGHF@EEFFA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U
10 | ERR156632.1508798	83	17	3006	29	1S4M1D95M	=	2587	-518	CCCCAAGCAGCAGCCGGGGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTCCCCAGATGCCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCT	<'&*(-+/?*88'-%%(((+KB/N.G)9.5E39>/;,F</*?*3K20GK703/('0'1G9)/,'2KIL6A8.G?I8LFC@>BHLI?CKH=BJ?FEE==DA	MD:Z:4^C6C0A2T1T36G8G36	RG:Z:rg	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M
11 | ERR243091.881299	83	17	3491	60	100M	=	3174	-416	CTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAA	C5;=CAAEFDFEEEEBCI;JFIKHGHGHIIKGEKGJIGGIJG=GDIKGFIHIJEIHJFFFFDDDAI>IDJDFGFEIFGHGIFGFJFIDFGEHGGDB@A@?	X0:i:1	X1:i:0	MD:Z:96G3	RG:Z:rg	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U
12 | ERR013140.23480670	133	17	3771	0	35M73S	=	3771	0	TTCTCATCAATCCCTCATCTCTTATAACCATTTCGGTCCTTTCGGCCCTACAGCCACCTTGTTTATACTTGGTAAGACCCACACCACTCGCCAACTTACTCTACTCCC	8+7?5>09:),/%81,$,7<+?)+1+*+),3%5+)#%(4B%$&'%'/*@,)*%%&,%(/0%-&$$*$-,$3*.%/$:%$+.$*%&+.,.%%,%(%7(-.-',1*6%&$	XC:i:35	RG:Z:rg
13 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn02_exp-a.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.0	SO:coordinate
 2 | @SQ	SN:17	LN:4200	SP:Human
 3 | @RG	ID:rg	SM:sample
 4 | ERR013140.3521432	99	17	1	29	22S86M	=	226	313	AGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCA	@AEDGBHIIIIIFJGIKHGHIJ!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MD:Z:86	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@iidijgijijfjkkhegjkkbiihcdeegjgdggihhhcidddidhjfihgbfjgejedXaach`i`geS^cd_hYccSWGWUc\]
 5 | ERR156632.12704932	163	17	1	29	36S64M	=	195	293	TGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTG	BFAFGFEIGFEFHHEIDKJGHHHJIIE=@KKGGKJG!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MD:Z:64	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@hakklejlchhgijjgedkkkjehglghgghgkjiebgeihi`hc\igjefgihgjjbgY_gc^
 6 | ERR156632.9601178	99	17	1	29	62S38M	=	279	377	CTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGA	DEEEIIHHKIJILKHLHIKEKHHMKLKKJGKKKKLKLFIHEKIKL=KLJLKIILHKMH9LJJ!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MD:Z:38	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@iikgkgiijiijlkjic]lijkdghfghg\eebge]ad
 7 | ERR162872.21706338	99	17	1	29	10S90M	=	246	344	CTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCA	BHBFH<EIFG!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MD:Z:90	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	ZQ:Z:@@@@@@@@@@ffiedfiiih^iijkcf`gijihhhkgebih`jjdijhigahgiaijcigjljifikjghfiWhfgjk\ifeWjbgjjYg`cShhceeea
 8 | ERR013140.13475139	99	17	2401	60	88M20S	=	2680	386	AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGCGTTTGAGGCTGCTGT	;;>BEEIHHHICFJIFKGHIKJHII>DBC:CE>A8C>C>7DBA=BEDDB4=9;:<C><??>@=;@D@@=B@E.3?972<>6@8=>?1$0:95%5%*1=8;0%4<228%	X0:i:1	X1:i:0	XC:i:88	MD:Z:88	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	ZQ:Z:EHG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 9 | ERR162875.26247502	83	17	2858	60	100M	=	2581	-376	ACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGAC	<DEHIIBHFHEKJKHBIMJLIHJIKIKKGIMH@LGJIHM=MDJILDKJKMMIJGHLLCLCJ;KKILKHHHKLICJKIHIIIIDDGJFCIHHGHF@EEFF>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
10 | ERR156632.1508798	83	17	3006	29	1S4M1D95M	=	2587	-518	CCCCAAGCAGCAGCCGGGGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTCCCCAGATGCCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCT	<!!!!-+/?*87'-%%(((+KB/N.G)9.5E39>/;,F</*?*3K20GK703/('0'1G9)/,'2KIL6A8.G?I8LFC@>BHLI?CKH=BJ?FEE==DA	MD:Z:4^C6C0A2T1T36G8G36	RG:Z:rg	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M	ZQ:Z:@FEIG@@@@@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
11 | ERR243091.881299	83	17	3491	60	100M	=	3174	-416	CTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAA	C5;=CAAEFDFEEEEBCI;JFIKHGHGHIIKGEKGJIGGIJG=GDIKGFIHIJEIHJFFFFDDDAI>IDJDFGFEIFGHGIFGFJFIDFGEH742+!!!!	X0:i:1	X1:i:0	MD:Z:96G3	RG:Z:rg	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@PSRW_`_^
12 | ERR013140.23480670	133	17	3771	0	35M73S	=	3771	0	TTCTCATCAATCCCTCATCTCTTATAACCATTTCGGTCCTTTCGGCCCTACAGCCACCTTGTTTATACTTGGTAAGACCCACACCACTCGCCAACTTACTCTACTCCC	8+7?5>09:),/%81,$,7<+?)+1+*+),3%5+)#%(4B%$&'%'/*@,)*%%&,%(/0%-&$$*$-,$3*.%/$:%$+.$*%&+.,.%%,%(%7(-.-',1*6%&$	XC:i:35	RG:Z:rg
13 | 


--------------------------------------------------------------------------------
/lib/htslib/test/realn02_exp-e.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.0	SO:coordinate
 2 | @SQ	SN:17	LN:4200	SP:Human
 3 | @RG	ID:rg	SM:sample
 4 | ERR013140.3521432	99	17	1	29	22S86M	=	226	313	AGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCA	@AEDGBHIIIIIFJGIKHGHIJJJEJKHJKJKGKLLIFHKLLCJJIDEFFHKHEHHJIIIDJEEEJEIKGJIHCGKHFKFE9BBDIAJAHF4?DE@I:DD48(86D=>	MD:Z:86	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@iidijgijijfjkkhegjkkbiihcdeegjgdggihhhcidddidhjfihgbfjgejedXaach`i`geS^cd_hYccSWGWUc\]
 5 | ERR156632.12704932	163	17	1	29	36S64M	=	195	293	TGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTG	BFAFGFEIGFEFHHEIDKJGHHHJIIE=@KKGGKJGIBLLMFKMDIIHJKKHFELLLKFIHMHIHHIHLKJFCHFJIJAID=JHKFGHJIHKKCH:@HD?	MD:Z:64	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@hakklejlchhgijjgedkkkjehglghgghgkjiebgeihi`hc\igjefgihgjjbgY_gc^
 6 | ERR156632.9601178	99	17	1	29	62S38M	=	279	377	CTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGA	DEEEIIHHKIJILKHLHIKEKHHMKLKKJGKKKKLKLFIHEKIKL=KLJLKIILHKMH9LJJJJLHLHJJKJJKMLKJD>MJKLEHIGHIH=FFCHF>BE	MD:Z:38	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@iikgkgiijiijlkjic]lijkdghfghg\eebge]ad
 7 | ERR162872.21706338	99	17	1	29	10S90M	=	246	344	CTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCA	BHBFH<EIFGGGJFEGJJJI?JJKLDGAHJKJIIILHFCJIAKKEJKIJHBIHJBJKDJHKMKJGJLKHIGJ8IGHKL=JGF8KCHKK:HAD4IIDFFFB	MD:Z:90	RG:Z:rg	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@ffiedfiiih^iijkcf`gijihhhkgebih`jjdijhigahgiaijcigjljifikjghfiWhfgjk\ifeWjbgjjYg`cShhceeea
 8 | ERR013140.13475139	99	17	2401	60	88M20S	=	2680	386	AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGCGTTTGAGGCTGCTGT	@CEBEEIHHHICFJIFKGHIKJHII>DBC:CE>A8C>C>7DBA=BEDDB4=9;:<C><??>@=;@D@@=B@E.3?972<>6@8=>?1$0:95%5%*1=8;0%4<228%	X0:i:1	X1:i:0	XC:i:88	MD:Z:88	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EHG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 9 | ERR162875.26247502	83	17	2858	60	100M	=	2581	-376	ACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGAC	<DEHIIBHFHEKJKHBIMJLIHJIKIKKGIMH@LGJIHM=MDJILDKJKMMIJGHLLCLCJ;KKILKHHHKLICJKIHIIIIDDGJFCIHHGHF@EEFFA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:rg	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
10 | ERR156632.1508798	83	17	3006	29	1S4M1D95M	=	2587	-518	CCCCAAGCAGCAGCCGGGGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTCCCCAGATGCCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCT	<'&*(-+/?*88'-%%(((+KB/N.G)9.5E39>/;,F</*?*3K20GK703/('0'1G9)/,'2KIL6A8.G?I8LFC@>BHLI?CKH=BJ?FEE==DA	MD:Z:4^C6C0A2T1T36G8G36	RG:Z:rg	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@FEIG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
11 | ERR243091.881299	83	17	3491	60	100M	=	3174	-416	CTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAA	C5;=CAAEFDFEEEEBCI;JFIKHGHGHIIKGEKGJIGGIJG=GDIKGFIHIJEIHJFFFFDDDAI>IDJDFGFEIFGHGIFGFJFIDFGEHGGDB@A@?	X0:i:1	X1:i:0	MD:Z:96G3	RG:Z:rg	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@PSRW_`_^
12 | ERR013140.23480670	133	17	3771	0	35M73S	=	3771	0	TTCTCATCAATCCCTCATCTCTTATAACCATTTCGGTCCTTTCGGCCCTACAGCCACCTTGTTTATACTTGGTAAGACCCACACCACTCGCCAACTTACTCTACTCCC	8+7?5>09:),/%81,$,7<+?)+1+*+),3%5+)#%(4B%$&'%'/*@,)*%%&,%(/0%-&$$*$-,$3*.%/$:%$+.$*%&+.,.%%,%(%7(-.-',1*6%&$	XC:i:35	RG:Z:rg
13 | 


--------------------------------------------------------------------------------
/lib/htslib/test/tabix/bed_file.bed:
--------------------------------------------------------------------------------
 1 | # The MIT License
 2 | #
 3 | # Copyright (c) 2017 Genome Research Ltd.
 4 | #
 5 | # Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | # of this software and associated documentation files (the "Software"), to deal
 7 | # in the Software without restriction, including without limitation the rights
 8 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | # copies of the Software, and to permit persons to whom the Software is
10 | # furnished to do so, subject to the following conditions:
11 | #
12 | # The above copyright notice and this permission notice shall be included in
13 | # all copies or substantial portions of the Software.
14 | #
15 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
21 | # THE SOFTWARE.
22 | #
23 | # Bed format information: https://genome.ucsc.edu/FAQ/FAQformat.html
24 | #
25 | X	1000	1100	X1	500	+	1000	1100	255,0,0
26 | X	1200	1300	X2	500	+	1200	1300	255,0,0
27 | X	1400	1500	X3	500	+	1400	1500	255,0,0
28 | X	1600	1700	X4	500	+	1600	1700	255,0,0
29 | X	1800	1900	X5	500	+	1800	1900	255,0,0
30 | Y	100000	100900	Y1	600	+	100000	100900	255,0,0
31 | Y	100200	100700	Y2	600	+	100200	100700	255,0,0
32 | Y	100400	100500	Y3	600	+	100400	100500	255,0,0
33 | Y	100600	100700	Y4	600	+	100600	100700	255,0,0
34 | Y	100800	100900	Y5	600	+	100800	100900	255,0,0
35 | Z	100000	100001	Z1	600	+	100000	100001	255,0,0
36 | Z	100002	100003	Z2	600	+	100002	100003	255,0,0
37 | Z	100004	100005	Z3	600	+	100004	100005	255,0,0
38 | Z	100006	100007	Z4	600	+	100006	100007	255,0,0
39 | Z	100008	100009	Z5	600	+	100008	100009	255,0,0
40 | 


--------------------------------------------------------------------------------
/lib/htslib/test/tabix/large_chr.vcf:
--------------------------------------------------------------------------------
 1 | ##fileformat=VCFv4.2
 2 | ##reference=file:///seq/references/long_chrom.fasta
 3 | ##FILTER=<ID=PASS,Description="All filters passed">
 4 | ##contig=<ID=chr11,length=116870911>
 5 | ##contig=<ID=chr20,length=2147483647>
 6 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
 7 | chr11	2343543	.	A	.	999	PASS	.
 8 | chr11	5464562	.	C	T	999	PASS	.
 9 | chr11	116870911	.	C	G	999	PASS	.
10 | chr20	76962	.	T	C	999	PASS	.
11 | chr20	126310	.	ACC	A	999	PASS	.
12 | chr20	138125	.	G	T	999	PASS	.
13 | chr20	138148	.	C	T	999	PASS	.
14 | chr20	271225	.	T	TTTA,TA	999	PASS	.
15 | chr20	304568	.	C	T	999	PASS	.
16 | chr20	620255100	.	AG	T	999	PASS	.
17 | chr20	630255200	.	G	C	999	PASS	.
18 | chr20	2147483647	.	A	T	999	PASS	.
19 | 


--------------------------------------------------------------------------------
/lib/htslib/test/tabix/tabix.tst:
--------------------------------------------------------------------------------
 1 | #    Copyright (C) 2017 Genome Research Ltd.
 2 | #
 3 | #    Author: Robert Davies <rmd@sanger.ac.uk>
 4 | #
 5 | # Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | # of this software and associated documentation files (the "Software"), to deal
 7 | # in the Software without restriction, including without limitation the rights
 8 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | # copies of the Software, and to permit persons to whom the Software is
10 | # furnished to do so, subject to the following conditions:
11 | #
12 | # The above copyright notice and this permission notice shall be included in
13 | # all copies or substantial portions of the Software.
14 | #
15 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | # DEALINGS IN THE SOFTWARE.
22 | 
23 | # First field:
24 | #   INIT = initialisation, not counted in testing
25 | #   P = expected to pass (zero return; expected output matches, if present)
26 | #   N = expected to return non-zero
27 | #   F = expected to fail
28 | #
29 | # Second field (P/N/F only):
30 | #   Filename of expected output.  If '.', output is not checked
31 | #
32 | # Rest:
33 | #   Command to execute.  $bgzip and $tabix are replaced with the path to
34 | # bgzip and tabix. 
35 | 
36 | # TBI index on VCF
37 | INIT $bgzip -c vcf_file.vcf > vcf_file.tbi.tmp.vcf.gz
38 | P . $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
39 | P vcf_file.1.3000151.out $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
40 | P vcf_file.2.3199812.out $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
41 | 
42 | # CSI index on VCF
43 | INIT $bgzip -c vcf_file.vcf > vcf_file.csi.tmp.vcf.gz
44 | P . $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
45 | P vcf_file.1.3000151.out $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
46 | P vcf_file.2.3199812.out $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
47 | 
48 | # VCF file with chromosome > 2^29-1 bases long
49 | # TBI cannot index this file, so building the index should fail
50 | INIT $bgzip -c large_chr.vcf > large_chr.tmp.vcf.gz
51 | N . $tabix -f -p vcf large_chr.tmp.vcf.gz
52 | 
53 | # CSI can handle positions > 2^29-1, so building should work
54 | P . $tabix -f -C -p vcf large_chr.tmp.vcf.gz
55 | P large_chr.20.1.2147483647.out $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
56 | 
57 | # TBI index on BED
58 | INIT $bgzip -c bed_file.bed > bed_file.tbi.tmp.bed.gz
59 | P . $tabix -f -p bed bed_file.tbi.tmp.bed.gz
60 | P bed_file.Y.100200.out $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
61 | 
62 | # TBI index on GFF3
63 | INIT $bgzip -c gff_file.gff > gff_file.tbi.tmp.gff.gz
64 | P . $tabix -f -p gff gff_file.tbi.tmp.gff.gz
65 | P gff_file.X.2934832.2935190.out $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190
66 | 


--------------------------------------------------------------------------------
/lib/htslib/test/tabix/vcf_file.vcf:
--------------------------------------------------------------------------------
 1 | ##fileformat=VCFv4.1
 2 | ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
 3 | ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
 4 | ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
 5 | ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 6 | ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 7 | ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
 8 | ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
 9 | ##FILTER=<ID=q10,Description="Quality below 10">
10 | ##FILTER=<ID=test,Description="Testing filter">
11 | ##contig=<ID=1,assembly=b37,length=249250621>
12 | ##contig=<ID=2,assembly=b37,length=249250621>
13 | ##contig=<ID=3,assembly=b37,length=198022430>
14 | ##contig=<ID=4,assembly=b37,length=191154276>
15 | ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
16 | ##readme=AAAAAA
17 | ##readme=BBBBBB
18 | ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
19 | ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
20 | ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
21 | ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
22 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
23 | 1	3000150	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
24 | 1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
25 | 1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
26 | 1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
27 | 1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
28 | 1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
29 | 1	3157410	.	GA	G	90.6	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
30 | 1	3162006	.	GAA	G	60.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:212:22	0/1:212:22
31 | 1	3177144	.	G	T	45	PASS	AN=4;AC=2	GT:GQ:DP	0/0:150:30	1/1:150:30
32 | 1	3177144	.	G	.	45	PASS	AN=4;AC=0	GT:GQ:DP	0/0:150:30	0/0:150:30
33 | 1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:10
34 | 2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:26	1/2:322:26
35 | 3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:91:26	1/2:91:26
36 | 4	3258448	.	TACACACAC	T	.	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
37 | 


--------------------------------------------------------------------------------
/lib/htslib/test/test-logging.pl:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env perl
 2 | #
 3 | #    Copyright (C) 2017 Genome Research Ltd.
 4 | #
 5 | #    Author: Anders Kaplan
 6 | #
 7 | # Permission is hereby granted, free of charge, to any person obtaining a copy
 8 | # of this software and associated documentation files (the "Software"), to deal
 9 | # in the Software without restriction, including without limitation the rights
10 | # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 | # copies of the Software, and to permit persons to whom the Software is
12 | # furnished to do so, subject to the following conditions:
13 | #
14 | # The above copyright notice and this permission notice shall be included in
15 | # all copies or substantial portions of the Software.
16 | #
17 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 | # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 | # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 | # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 | # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 | # DEALINGS IN THE SOFTWARE.
24 | 
25 | use strict;
26 | 
27 | my $log_message_count = 0;
28 | my $file_count = 0;
29 | my $failure_count = 0;
30 | 
31 | sub check_log_message
32 | {
33 |   my ($message, $filename, $line_num) = @_;
34 |   $log_message_count++;
35 | 
36 |   unless ($message =~ /^\"([A-Z]|%s)/)
37 |   {
38 |     print "$filename line $line_num:\n";
39 |     print "Log message should begin with a capital letter: $message.\n";
40 |     $failure_count++;
41 |   }
42 | 
43 |   if ($message =~ /\\n\"$/)
44 |   {
45 |     print "$filename line $line_num:\n";
46 |     print "Log message should NOT end with a newline: $message.\n";
47 |     $failure_count++;
48 |   }
49 | 
50 |   if ($message =~ /\.\"$/)
51 |   {
52 |     print "$filename line $line_num:\n";
53 |     print "Log message should NOT end with a full stop: $message.\n";
54 |     $failure_count++;
55 |   }
56 | }
57 | 
58 | sub check_file
59 | {
60 |   my ($filename) = @_;
61 |   $file_count++;
62 | 
63 |   open(my $fh, '<', $filename) or die "Could not open $filename.";
64 |   my $line_num = 1;
65 |   my $line = <$fh>;
66 |   while ($line)
67 |   {
68 |     if ($line =~ /hts_log_\w+\s*\(\s*(\"[^\"]*\")/)
69 |     {
70 |       unless ($line =~ /\\n\"\s*$/) # string constant continues on next line
71 |       {
72 |         check_log_message($1, $filename, $line_num);
73 |       }
74 |     }
75 | 
76 |     $line_num++;
77 |     $line = <$fh>;
78 |   }
79 | }
80 | 
81 | sub check_dir
82 | {
83 |   my ($path) = @_;
84 |   foreach my $filename (glob("$path/*.c"))
85 |   {
86 |     check_file($filename);
87 |   }
88 | }
89 | 
90 | check_dir("..");
91 | check_dir("../cram");
92 | 
93 | print "$file_count files scanned\n";
94 | print "$log_message_count log messages checked\n";
95 | print "$failure_count errors found\n";
96 | exit($failure_count > 0);
97 | 


--------------------------------------------------------------------------------
/lib/htslib/test/test-vcf-hdr-in.vcf:
--------------------------------------------------------------------------------
 1 | ##fileformat=VCFv4.1
 2 | ##fileDate=20150126
 3 | ##reference=hs37d5
 4 | ##phasing=partial
 5 | ##FILTER=<ID=INDEL_SPECIFIC_FILTERS,Description="QD < 2.0 || ReadPosRankSum < -20.0 || InbreedingCoeff < -0.8 || FS > 200.0">
 6 | ##FILTER=<ID=LowQual,Description="Low quality">
 7 | ##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -6.6778 <= x < -0.6832">
 8 | ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -36469.5723">
 9 | ##INFO=<ID=TRAILING,Number=.,Type=Integer,Description="This line contains trailing spaces for testing purposes">               
10 | ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
11 | ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
12 | ##FORMAT=<ID=GQ,Number=1,Type=Integer,EmptyWithSpace= ,Description="Genotype Quality">
13 | ##FORMAT=<ID=GATK,Number=1, Type  =   String    ,     Description="Genotype as called by GATK. Always a diploid call. All other genotype stats based on this genotype.">
14 | ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype after Personalis post-processing to match detected chromosome counts.">
15 | #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001
16 | 1	12065947	PTV001	C	T,A	29	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:19
17 | 1	109817590	PTV002	G	T	77	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:20
18 | 1	153791300	PTV003	CTG	C	81	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:21
19 | 1	156104666	PTV004	TTGAGAGCCGGCTGGCGGAT	TCC	30	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:22
20 | 1	156108541	PTV005	G	GG	31	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:23
21 | 1	161279695	PTV006	T	C,A	32	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:24
22 | 1	169519049	PTV007	T	.	35	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:24
23 | 1	226125468	PTV097	G	A	99	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:109
24 | 16	2103394	PTV056	C	T	68	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:72
25 | 4	31789170	PTV021	G	.	77	PASS	.	GT:GATK:AD:DP:GQ	0/1:0/1:3,2:5:38
26 | 


--------------------------------------------------------------------------------
/lib/htslib/test/thrash_threads1.c:
--------------------------------------------------------------------------------
 1 | /* The MIT/Expat License
 2 | 
 3 | Copyright (C) 2017 Genome Research Ltd.
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in
13 | all copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | DEALINGS IN THE SOFTWARE.
22 |  */
23 | // Test extreme rapid turnover of readers, to check for
24 | // race conditions between reader thread launching and file close.
25 | 
26 | #include <config.h>
27 | 
28 | #include <stdio.h>
29 | #include <unistd.h>
30 | #include <stdlib.h>
31 | #include "htslib/bgzf.h"
32 | 
33 | int main(int argc, char *argv[]) {
34 |     if (argc <= 1) {
35 |         fprintf(stderr, "Usage: thrash_threads1 input.bam\n");
36 |         exit(1);
37 |     }
38 | 
39 |     int i;
40 |     for (i = 0; i < 10000; i++) {
41 |         printf("i=%d\n", i);
42 |         BGZF *fpin  = bgzf_open(argv[1], "r");
43 |         bgzf_mt(fpin, 2, 256);
44 |         if (bgzf_close(fpin) < 0) abort();
45 |     }
46 |     return 0;
47 | }
48 | 


--------------------------------------------------------------------------------
/lib/htslib/test/thrash_threads2.c:
--------------------------------------------------------------------------------
 1 | /* The MIT/Expat License
 2 | 
 3 | Copyright (C) 2017 Genome Research Ltd.
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in
13 | all copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | DEALINGS IN THE SOFTWARE.
22 |  */
23 | // Test extreme rapid turnover of writers, to check for
24 | // race conditions between reader thread launching and file close.
25 | 
26 | #include <config.h>
27 | 
28 | #include <stdio.h>
29 | #include <unistd.h>
30 | #include <stdlib.h>
31 | #include "htslib/bgzf.h"
32 | #include "htslib/thread_pool.h"
33 | 
34 | int main(int argc, char *argv[]) {
35 |     int i;
36 |     for (i = 0; i < 1000; i++) {
37 |         printf("i=%d\n", i);
38 |         BGZF *fp  = bgzf_open("/dev/null", "w");
39 |         bgzf_mt(fp, 8, 256);
40 |         if (bgzf_close(fp))
41 |             abort();
42 |     }
43 | 
44 |     return 0;
45 | }
46 | 


--------------------------------------------------------------------------------
/lib/htslib/test/thrash_threads3.c:
--------------------------------------------------------------------------------
 1 | /* The MIT/Expat License
 2 | 
 3 | Copyright (C) 2017 Genome Research Ltd.
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in
13 | all copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | DEALINGS IN THE SOFTWARE.
22 |  */
23 | // Simple open,read,close thrash.
24 | 
25 | #include <config.h>
26 | 
27 | #include <stdio.h>
28 | #include <unistd.h>
29 | #include <stdlib.h>
30 | #include "htslib/bgzf.h"
31 | 
32 | int main(int argc, char *argv[]) {
33 |     char buf[1000000];
34 |     int i;
35 | 
36 |     if (argc <= 1) {
37 |         fprintf(stderr, "Usage: thrash_threads3 input.bam\n");
38 |         exit(1);
39 |     }
40 | 
41 |     for (i = 0; i < 10000; i++) {
42 |         printf("i=%d\n", i);
43 |         BGZF *fpin  = bgzf_open(argv[1], "r");
44 |         if (bgzf_read(fpin, buf, i*10) < 0) abort();
45 |         bgzf_mt(fpin, 8, 256);
46 |         if (bgzf_read(fpin, buf, i*10) < 0) abort();
47 |         if (bgzf_close(fpin) < 0) abort();
48 |     }
49 |     return 0;
50 | }
51 | 


--------------------------------------------------------------------------------
/lib/htslib/test/thrash_threads4.c:
--------------------------------------------------------------------------------
 1 | /* The MIT/Expat License
 2 | 
 3 | Copyright (C) 2017 Genome Research Ltd.
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in
13 | all copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | DEALINGS IN THE SOFTWARE.
22 |  */
23 | // Spam seeks
24 | #include <config.h>
25 | 
26 | #include <stdlib.h>
27 | #include <stdio.h>
28 | #include <unistd.h>
29 | #include "htslib/bgzf.h"
30 | #include "htslib/thread_pool.h"
31 | 
32 | int main(int argc, char *argv[]) {
33 |     if (argc <= 1) {
34 |         fprintf(stderr, "Usage: thrash_threads4 input.bam\n");
35 |         exit(1);
36 |     }
37 | 
38 |     // Find a valid seek location ~64M into the file
39 |     int i;
40 |     BGZF *fpin  = bgzf_open(argv[1], "r");
41 |     char buf[65536];
42 |     for (i = 0; i < 1000; i++)
43 |         if (bgzf_read(fpin, buf, 65536) < 0)
44 |             abort();
45 |     int64_t pos = bgzf_tell(fpin);
46 |     bgzf_close(fpin);
47 | 
48 | #define N 1000
49 | 
50 |     // Spam seeks
51 |     for (i = 0; i < 1000; i++) {
52 |         printf("i=%d\n", i);
53 |         fpin  = bgzf_open(argv[1], "r");
54 |         bgzf_mt(fpin, 8, 256);
55 |         if (bgzf_seek(fpin, pos, SEEK_SET) < 0) puts("!");//abort();
56 |         usleep(N);
57 |         //if (bgzf_read(fpin, buf, 65536) < 0) abort();
58 |         //write(1, buf, 65536);
59 |         if (bgzf_seek(fpin, 0LL, SEEK_SET) < 0) puts("!");//abort();
60 |         usleep(N);
61 |         //if (bgzf_read(fpin, buf, 65536) < 0) abort();
62 |         //write(1, buf, 65536);
63 |         if (bgzf_close(fpin))
64 |             abort();
65 |     }
66 | 
67 |     return 0;
68 | }
69 | 


--------------------------------------------------------------------------------
/lib/htslib/test/thrash_threads5.c:
--------------------------------------------------------------------------------
 1 | /* The MIT/Expat License
 2 | 
 3 | Copyright (C) 2017 Genome Research Ltd.
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in
13 | all copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
18 | THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21 | DEALINGS IN THE SOFTWARE.
22 |  */
23 | // A basic 'zcat filename [N-threads]'
24 | 
25 | #include <config.h>
26 | 
27 | #include <stdio.h>
28 | #include <stdlib.h>
29 | #include <unistd.h>
30 | #include "htslib/bgzf.h"
31 | #include "htslib/thread_pool.h"
32 | 
33 | #define N 1000
34 | int main(int argc, char *argv[]) {
35 |     char buf[N];
36 |     ssize_t l, t = 0;
37 | 
38 |     if (argc < 2 || isatty(STDOUT_FILENO)) {
39 |         fprintf(stderr,
40 |                 "Usage: thrash_threads5 input.bam num_threads | md5sum\n");
41 |         exit(1);
42 |     }
43 | 
44 |     BGZF *fpin  = bgzf_open(argv[1], "r");
45 |     hts_tpool *p = NULL;
46 |     if (argc > 2) {
47 |         p = hts_tpool_init(atoi(argv[2]));
48 |         bgzf_thread_pool(fpin,  p, 0);
49 |     }
50 |     int n = rand()%(N-1)+1;
51 |     while ((l = bgzf_read(fpin, buf, n)) > 0) {
52 |         if (l != write(STDOUT_FILENO, buf, l)) abort();
53 |         t += l;
54 |         if (l != n) {
55 |             fprintf(stderr, "expected %d bytes, got %d\n", n, (int)l);
56 |             break;
57 |         }
58 |         n = rand()%(N-1)+1;
59 |     }
60 |     fprintf(stderr, "close=%d\n", (int)bgzf_close(fpin));
61 |     if (p) hts_tpool_destroy(p);
62 | 
63 |     fprintf(stderr, "wrote %d bytes\n", (int)t);
64 | 
65 |     return 0;
66 | }
67 | 


--------------------------------------------------------------------------------
/lib/htslib/test/thread_pool.md:
--------------------------------------------------------------------------------
 1 | Thread pool tests
 2 | =================
 3 | The thread_pool.c file has a built-in test program which is enabled when compiling with TEST_MAIN defined. The test program can be run in four different modes by giving a command-line parameter: unordered, ordered1, ordered2, and pipe. The modes and their expected outputs are described below.
 4 | 
 5 | unordered
 6 | ---------
 7 | Dispatches TASK_SIZE (=1000) jobs to the thread pool and waits for them to finish. The job index (0..TASK_SIZE-1) is passed as a parameter. The job function is doit_square_u, which sleeps for a while and then prints the square of its input parameter to stdout.
 8 | 
 9 | Expected output when n = 1:
10 | ```
11 | RESULT: 0
12 | ...
13 | RESULT: 998001
14 | ```
15 | 
16 | Expected output when n > 1: same, but in jumbled up order.
17 | 
18 | ordered1
19 | --------
20 | Dispatches TASK_SIZE (=1000) jobs to the thread pool in non-blocking mode. Results are returned on the result queue and are pulled in order. The job index (0..TASK_SIZE-1) is passed as a parameter. The job function is doit_square, which sleeps for a while and then returns the square of its input parameter as a result. Some of the jobs take way longer than the others to finish.
21 | 
22 | The expected output is the results printed in order, regardless of n.
23 | 
24 | ordered2
25 | --------
26 | Starts a dispatcher thread which dispatches jobs to the thread pool. After all regular jobs have been dispatched, a sentinel job follows where the input parameter is set to -1, which receives special handling in doit_square to return the -1 as the result.
27 | 
28 | Results are consumed on the main thread using hts_tpool_next_result_wait, until the end-of-job marker is found.
29 | 
30 | The expected output is the results printed in order, regardless of n.
31 | 
32 | pipe
33 | ----
34 | This program uses one thread pool (hts_tpool) and three queues (hts_tpool_process) shared across threads using a pipe_opt struct. There are four threads: input, stage1to2, stage2to3, and output.
35 | 
36 | The input thread (pipe_input_thread procedure) dispatches jobs to the thread pool with the job number (1..TASK_SIZE) and an end-of-job flag as parameters. The jobs are executed by the pipe_stage1 procedure, which multiplies by 256 and sleeps for a short while.
37 | 
38 | The stage1to2 thread (pipe_stage1to2 procedure) pulls results from the first queue (q1) and passes them to new jobs in the thread pool. These jobs are executed by the pipe_stage2 procedure, which does the same as pipe_stage1, only slower.
39 | 
40 | The stage2to3 thread is similar to the stage1to2 thread. It pulls from the second queue and dispatches new jobs to be executed by the pipe_stage3 procedure. pipe_stage3 is similar to pipe_stage1.
41 | 
42 | The output thread pulls from the third queue.
43 | 
44 | Expected output:
45 | ```
46 | I 00000001
47 | 1 00000100
48 | 2 00010000
49 | O 01000000
50 | ...
51 | I 000003e8
52 | 1 0003e800
53 | 2 03e80000
54 | O e8000000
55 | ```
56 | ...but not in order, because the input queues might be served in any order.
57 | 
58 | However, if only the lines from the output thread are printed, they should be in order regardless of the number of threads.
59 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#blank.sam:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/xx#blank.sam


--------------------------------------------------------------------------------
/lib/htslib/test/xx#large_aux2.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:xx	LN:20
 2 | a1	0	xx	1	1	1M	*	0	0	A	#	aa:i:1
 3 | a2	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1
 4 | a3	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1
 5 | a4	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1
 6 | a5	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1	ae:i:1
 7 | a6	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1	ae:i:1	af:i:1
 8 | a7	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1	ae:i:1	af:i:1	ag:i:1
 9 | a8	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1	ae:i:1	af:i:1	ag:i:1	ah:i:1
10 | a9	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1	ae:i:1	af:i:1	ag:i:1	ah:i:1	ai:i:1
11 | aA	0	xx	1	1	1M	*	0	0	A	#	aa:i:1	ab:i:1	ac:i:1	ad:i:1	ae:i:1	af:i:1	ag:i:1	ah:i:1	ai:i:1	aj:i:1
12 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#large_aux_java.cram:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/lib/htslib/test/xx#large_aux_java.cram


--------------------------------------------------------------------------------
/lib/htslib/test/xx#minimal.sam:
--------------------------------------------------------------------------------
 1 | @SQ	SN:xx	LN:20
 2 | @SQ	SN:yy	LN:20
 3 | a0	16	xx	4	1	10H	*	0	0	*	*
 4 | a1	16	xx	4	1	5H0M5H	*	0	0	*	*
 5 | a2	16	xx	4	1	5H0I10M0D5H	*	0	0	*	*
 6 | A0	16	yy	4	1	0H	*	0	0	*	*
 7 | A1	16	yy	4	1	0I	*	0	0	*	*
 8 | A2	16	yy	4	1	0D	*	0	0	*	*
 9 | A3	16	yy	4	1	0M	*	0	0	*	*
10 | A4	16	yy	4	1	0P	*	0	0	*	*
11 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#pair.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:xx	LN:20
2 | a1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
3 | b1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
4 | c1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
5 | a1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
6 | b1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
7 | c1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
8 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#repeated.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:xx	LN:20
2 | S	67	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
3 | S	131	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
4 | S	67	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
5 | S	131	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
6 | S	67	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
7 | S	131	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
8 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#rg.sam:
--------------------------------------------------------------------------------
 1 | @HD	VN:1.4	SO:coordinate
 2 | @SQ	SN:xx	LN:20	AS:?	SP:?	UR:?	M5:bbf4de6d8497a119dda6e074521643dc
 3 | @RG	ID:x1	SM:x1
 4 | @RG	ID:x2	SM:x2	LB:x	PG:foo:bar	PI:1111
 5 | @PG	ID:emacs	PN:emacs	VN:23.1.1
 6 | @CO	also test
 7 | @CO	other	headers
 8 | a1	16	xx	1	1	10M	*	0	0	AAAAAAAAAA	**********	RG:Z:x1
 9 | b1	16	xx	1	1	10M	*	0	0	AAAAAAAAAA	**********	RG:Z:x2
10 | c1	16	xx	1	1	10M	*	0	0	AAAAAAAAAA	**********
11 | a2	16	xx	11	1	10M	*	0	0	TTTTTTTTTT	**********	RG:Z:x1
12 | b2	16	xx	11	1	10M	*	0	0	TTTTTTTTTT	**********	RG:Z:x2
13 | c2	16	xx	11	1	10M	*	0	0	TTTTTTTTTT	**********
14 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#tlen.sam:
--------------------------------------------------------------------------------
 1 | @CO	xx has been encoded using the SAM spec; leftmost to rightmost
 2 | @CO	yy has been encoded using bwa/picard methods; 5' to 3'
 3 | @CO
 4 | @CO	00000000011111111112
 5 | @CO	12345678901234567890
 6 | @CO	AAAAAAAAAATTTTTTTTTT
 7 | @CO	1>>>>          <<<<2   x1
 8 | @CO	
 9 | @CO	      1>>>>    	       x2
10 | @CO	         <<<<2
11 | @CO	
12 | @CO	         1>>>>	       x3 (7..15 vs 10..11)
13 | @CO	      <<<<2
14 | @CO	
15 | @CO	<<<<2          1>>>>   x4 (1..20 vs 16..5)
16 | @CO
17 | @SQ	SN:xx	LN:20
18 | @SQ	SN:yy	LN:20
19 | x1	99	xx	1	1	5M	=	16	20	AAAAA	*****
20 | x1	147	xx	16	1	5M	=	1	-20	TTTTT	*****
21 | x2	99	xx	7	1	5M	=	10	8	AAAAT	*****
22 | x2	147	xx	10	1	5M	=	7	-8	ATTTT	*****
23 | x3	147	xx	7	1	5M	=	10	8	AAAAT	*****
24 | x3	99	xx	10	1	5M	=	7	-8	ATTTT	*****
25 | x4	147	xx	1	1	5M	=	16	20	AAAAA	*****
26 | x4	99	xx	16	1	5M	=	1	-20	TTTTT	*****
27 | y1	99	yy	1	1	5M	=	16	20	AAAAA	*****
28 | y1	147	yy	16	1	5M	=	1	-20	TTTTT	*****
29 | y2	99	yy	7	1	5M	=	10	8	AAAAT	*****
30 | y2	147	yy	10	1	5M	=	7	-8	ATTTT	*****
31 | y3	147	yy	7	1	5M	=	10	-2	AAAAT	*****
32 | y3	99	yy	10	1	5M	=	7	2	ATTTT	*****
33 | y4	147	yy	1	1	5M	=	16	10	AAAAA	*****
34 | y4	99	yy	16	1	5M	=	1	-10	TTTTT	*****
35 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#tlen2.sam:
--------------------------------------------------------------------------------
 1 | @CO	As per xx#tlen.sam but every read is unsorted with partner
 2 | @CO	
 3 | @CO	xx has been encoded using the SAM spec; leftmost to rightmost
 4 | @CO	yy has been encoded using bwa/picard methods; 5' to 3'
 5 | @CO
 6 | @CO	00000000011111111112
 7 | @CO	12345678901234567890
 8 | @CO	AAAAAAAAAATTTTTTTTTT
 9 | @CO	1>>>>          <<<<2   x1
10 | @CO	
11 | @CO	      1>>>>    	       x2
12 | @CO	         <<<<2
13 | @CO	
14 | @CO	         1>>>>	       x3 (7..15 vs 10..11)
15 | @CO	      <<<<2
16 | @CO	
17 | @CO	<<<<2          1>>>>   x4 (1..20 vs 16..5)
18 | @CO
19 | @SQ	SN:xx	LN:20
20 | @SQ	SN:yy	LN:20
21 | x1	147	xx	16	1	5M	=	1	-20	TTTTT	*****
22 | x1	99	xx	1	1	5M	=	16	20	AAAAA	*****
23 | x2	147	xx	10	1	5M	=	7	-8	ATTTT	*****
24 | x2	99	xx	7	1	5M	=	10	8	AAAAT	*****
25 | x3	99	xx	10	1	5M	=	7	-8	ATTTT	*****
26 | x3	147	xx	7	1	5M	=	10	8	AAAAT	*****
27 | x4	99	xx	16	1	5M	=	1	-20	TTTTT	*****
28 | x4	147	xx	1	1	5M	=	16	20	AAAAA	*****
29 | y1	147	yy	16	1	5M	=	1	-20	TTTTT	*****
30 | y1	99	yy	1	1	5M	=	16	20	AAAAA	*****
31 | y2	147	yy	10	1	5M	=	7	-8	ATTTT	*****
32 | y2	99	yy	7	1	5M	=	10	8	AAAAT	*****
33 | y3	99	yy	10	1	5M	=	7	2	ATTTT	*****
34 | y3	147	yy	7	1	5M	=	10	-2	AAAAT	*****
35 | y4	99	yy	16	1	5M	=	1	-10	TTTTT	*****
36 | y4	147	yy	1	1	5M	=	16	10	AAAAA	*****
37 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#triplet.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:xx	LN:20
2 | @SQ	SN:yy	LN:20
3 | a1	67	xx	1	1	10M	=	6	20	AAAAAAAAAA	**********
4 | a1	35	xx	6	1	10M	=	11	-20	AAAAATTTTT	**********
5 | a1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
6 | a1	67	yy	1	1	10M	=	6	15	AAAAAAAAAA	**********
7 | a1	3	yy	6	1	10M	=	1	-15	AAAAATTTTT	**********
8 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx#unsorted.sam:
--------------------------------------------------------------------------------
1 | @SQ	SN:xx	LN:20
2 | @SQ	SN:yy	LN:20
3 | b1	147	yy	11	1	10M	=	1	-20	TTTTTTTTTT	**********
4 | a1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
5 | a1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
6 | b1	99	yy	1	1	10M	=	11	20	AAAAAAAAAA	**********
7 | c1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
8 | c1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
9 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx.fa:
--------------------------------------------------------------------------------
1 | >xx
2 | AAAAAAAAAATTTTTTTTTT
3 | >yy
4 | AAAAAAAAAATTTTTTTTTT
5 | 
6 | 


--------------------------------------------------------------------------------
/lib/htslib/test/xx.fa.fai:
--------------------------------------------------------------------------------
1 | xx	20	4	20	21
2 | yy	20	29	20	21
3 | 


--------------------------------------------------------------------------------
/lib/htslib/version.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/sh
 2 | 
 3 | # Master version, for use in tarballs or non-git source copies
 4 | VERSION=1.9
 5 | 
 6 | # If we have a git clone, then check against the current tag
 7 | if [ -e .git ]
 8 | then
 9 |     # If we ever get to 10.x this will need to be more liberal
10 |     VERSION=`git describe --match '[0-9].[0-9]*' --dirty`
11 | fi
12 | 
13 | # Numeric version is for use in .dylib or .so libraries
14 | #
15 | # Follows the same logic from the Makefile commit c2e93911
16 | # as non-numeric versions get bumped to patch level 255 to indicate
17 | # an unknown value.
18 | if [ "$1" = "numeric" ]
19 | then
20 |     v1=`expr "$VERSION" : '\([0-9]*\)'`
21 |     v2=`expr "$VERSION" : '[0-9]*.\([0-9]*\)'`
22 |     v3=`expr "$VERSION" : '[0-9]*.[0-9]*.\([0-9]*\)'`
23 |     if [ -z "`expr "$VERSION" : '^\([0-9.]*\)$'`" ]
24 |     then
25 | 	VERSION="$v1.$v2.255"
26 |     else
27 | 	VERSION="$v1.$v2${v3:+.}$v3"
28 |     fi
29 | fi
30 | 
31 | echo $VERSION
32 | 


--------------------------------------------------------------------------------
/lib/index.c:
--------------------------------------------------------------------------------
  1 | #define _GNU_SOURCE
  2 | #include <stdio.h>
  3 | #include <stdint.h>
  4 | #include <stdlib.h>
  5 | #include "index.h"
  6 | 
  7 | void read_index(char *file, index_tag **indexs, uint32_t *index_tag_size, void *f2bit){
  8 | 
  9 | 	char *line = NULL;
 10 | 	size_t len = 0;
 11 | 
 12 | 	FILE *lines = fopen(file, "r");
 13 | 
 14 | 	if (lines == NULL){
 15 | 		fprintf(stderr, "Failed open file [%s]!\n", file);
 16 | 		exit(1);
 17 | 	}
 18 | 
 19 | 	uint32_t name;
 20 | 	uint64_t offset; // may be overflow of max_value
 21 | 	uint32_t length;
 22 | 	while (getline(&line, &len, lines) != -1) {
 23 | 
 24 | 		sscanf(line, "%u\t%lu\t%u", &name, &offset, &length);//%hu\t
 25 | 
 26 | 		while (*index_tag_size <= name){
 27 | 			*index_tag_size += 65536;
 28 | 			*indexs = realloc(*indexs, *index_tag_size * sizeof(index_tag));// need pointer of pointer
 29 | 		}
 30 | 
 31 | 		(*indexs)[name].f2bit = f2bit;
 32 | 		(*indexs)[name].offset = offset;
 33 | 	}
 34 | 	free(line);
 35 | 	fclose(lines);
 36 | }
 37 | 
 38 | 
 39 | void read_len_index(char *file, index_len_tag **indexs, uint32_t *index_tag_size, FILE *f2bit){
 40 | 
 41 | 	char *line = NULL;
 42 | 	size_t len = 0;
 43 | 
 44 | 	FILE *lines = fopen(file, "r");
 45 | 
 46 | 	if (lines == NULL){
 47 | 		fprintf(stderr, "Failed open file [%s]!\n", file);
 48 | 		exit(1);
 49 | 	}
 50 | 
 51 | 	uint32_t name;
 52 | 	uint64_t offset; // may be overflow of max_value
 53 | 	uint32_t length;
 54 | 	while (getline(&line, &len, lines) != -1) {
 55 | 
 56 | 		sscanf(line, "%u\t%lu\t%u", &name, &offset, &length);//%hu\t
 57 | 
 58 | 		while (*index_tag_size <= name){
 59 | 			*index_tag_size += 65536;
 60 | 			*indexs = realloc(*indexs, *index_tag_size * sizeof(index_len_tag));// need pointer of pointer
 61 | 		}
 62 | 
 63 | 		(*indexs)[name].f2bit = f2bit;
 64 | 		(*indexs)[name].offset = offset;
 65 | 		(*indexs)[name].length = length;
 66 | 	}
 67 | 	free(line);
 68 | 	fclose(lines);
 69 | }
 70 | 
 71 | idxs *init_index(FILE *fa){
 72 | 	FILE *f;
 73 | 	char idxf[1024];
 74 | 	char *file = NULL;
 75 | 	size_t len = 0;
 76 | 	ssize_t nread;
 77 | 	idxs *idx = malloc(sizeof(idxs));
 78 | 
 79 | 	idx->idxm = 65536;
 80 | 	idx->idx = malloc(idx->idxm * sizeof(index_len_tag));
 81 | 	idx->fai = 0;
 82 | 	idx->fam = 1024;
 83 | 	idx->fa = malloc(idx->fam * sizeof(FILE *));
 84 | 	while ((nread = getline(&file, &len, fa)) != -1) {
 85 | 		if (nread != 1 && file[0] != '#'){
 86 | 			file[nread - 1 ] = '\0';
 87 | 			f = fopen(file, "r");
 88 | 			if (f == NULL){
 89 | 				fprintf(stderr, "Failed open file [%s]\n", file);
 90 | 				exit(1);
 91 | 			}
 92 | 
 93 | 			idx->fa[idx->fai++] = f;
 94 | 			if (idx->fai >= idx->fam) {
 95 | 				idx->fam += 1024;
 96 | 				idx->fa = realloc(idx->fa, idx->fam * sizeof(FILE *));
 97 | 			}
 98 | 
 99 | 			nread = sprintf(idxf, "%s.idx", file);
100 | 			idxf[nread] = '\0';
101 | 			read_len_index(idxf, &idx->idx, &idx->idxm, f);
102 | 		}   
103 | 	}
104 | 	if (file) free(file);
105 | 	return idx;
106 | }
107 | 
108 | void destroy_index(idxs *idx){
109 | 	int i;
110 | 	for ( i = 0; i < idx->fai; i++){
111 | 		fclose(idx->fa[i]);
112 | 	}
113 | 	free (idx->fa);
114 | 	free(idx->idx);
115 | 	free (idx);
116 | }
117 | 
118 | 


--------------------------------------------------------------------------------
/lib/index.h:
--------------------------------------------------------------------------------
 1 | #include <stdint.h>
 2 | #include <stdio.h>
 3 | 
 4 | typedef struct {
 5 | 	void *f2bit;
 6 | 	uint64_t offset;
 7 | } index_tag;
 8 | 
 9 | typedef struct {
10 | 	FILE *f2bit;
11 | 	uint64_t offset;
12 | 	uint32_t length;
13 | } index_len_tag;
14 | 
15 | typedef struct {
16 | 	index_len_tag *idx;
17 | 	uint32_t idxm;
18 | 	FILE **fa;
19 | 	int fai;
20 | 	int fam;
21 | } idxs;
22 | 
23 | void read_index(char *file, index_tag **indexs, uint32_t *index_tag_size, void *f2bit);
24 | void read_len_index(char *file, index_len_tag **indexs, uint32_t *index_tag_size, FILE *f2bit);
25 | idxs *init_index(FILE *fa);
26 | void destroy_index(idxs *idx);
27 | 


--------------------------------------------------------------------------------
/lib/kit.c:
--------------------------------------------------------------------------------
  1 | #define  _GNU_SOURCE
  2 | #include <stdio.h>
  3 | #include <stdlib.h>
  4 | #include <stdint.h>
  5 | #include "bseq.h"
  6 | 
  7 | uint64_t calgs(const char *file){
  8 | 	gzFile fp; 
  9 | 	fp = gzopen(file, "r");
 10 | 	if (fp == NULL) {
 11 | 		fprintf(stderr, "Error! %s does not exist!", file); 
 12 | 		exit(1);
 13 | 	}
 14 | 	uint64_t gs = 0;
 15 | 	kseq_t *seq;
 16 | 	seq = kseq_init(fp);
 17 | 	while(kseq_r(seq) >= 0) {
 18 | 		gs += seq->seq.l;
 19 | 	}
 20 | 	kseq_destroy(seq);
 21 | 	gzclose(fp);
 22 | 	return gs;
 23 | }
 24 | 
 25 | ///////////////////////////////////
 26 | typedef struct record {
 27 | 	uint32_t *len;
 28 | 	unsigned int i, im;
 29 | } record;
 30 | 
 31 | static int cmp_uint(const void * a, const void * b){
 32 | 	return *(uint32_t *) b - *(uint32_t *) a;
 33 | }
 34 | 
 35 | void read_data_from_file(record *data, const char *file){
 36 | 	FILE *fp = fopen(file, "r");
 37 | 	if (fp == NULL) {
 38 | 		fprintf(stderr, "Error! %s does not exist!", file);
 39 | 		exit(1);
 40 | 	}
 41 | 
 42 | 	char *line = NULL;
 43 | 	size_t len = 0;
 44 | 	ssize_t ret, nread;
 45 | 	uint32_t name, length;
 46 | 	uint64_t offset;
 47 | 
 48 | 	while((nread = getline(&line, &len, fp)) != -1) {
 49 | 		ret = sscanf(line, "%u\t%lu\t%u", &name, &offset, &length);
 50 | 		if (ret >= 0){
 51 | 			data->len[data->i++] = length;
 52 | 			if (data->i >= data->im) {
 53 | 				data->im += 100000;
 54 | 				data->len = realloc(data->len, sizeof(uint32_t) * data->im);
 55 | 			}
 56 | 		}
 57 | 	}
 58 | 	if (line) free(line);
 59 | 	fclose (fp);
 60 | }
 61 | 
 62 | uint32_t cal_minlen_from_idx(char **files, const int file_count, const uint64_t total_len){
 63 | 	unsigned int i;
 64 | 	record data = {0};
 65 | 	data.im = 100000;
 66 | 	data.len = malloc(sizeof(uint32_t) * data.im);
 67 | 
 68 | 	for (i = 0; i < file_count; i++){
 69 | 		read_data_from_file(&data, files[i]);
 70 | 	}
 71 | 
 72 | 	qsort(data.len, data.i, sizeof(uint32_t), cmp_uint);
 73 | 	
 74 | 	uint64_t total;
 75 | 	for (i = total = 0; i < data.i && total < total_len; i ++) total += data.len[i];
 76 | 
 77 | 	total = i >= 1 ? data.len[i - 1] : 0;
 78 | 	free (data.len);
 79 | 	return (uint32_t) total;
 80 | }
 81 | 
 82 | // #include <libgen.h>
 83 | // int main(int argc, char *argv[])
 84 | // {
 85 | // 	// uint64_t gs = calgs(argv[1]);
 86 | // 	// printf("genome size: %lu bp\n", gs);
 87 | 
 88 | // 	char *path = dirname(strdup(argv[optind]));
 89 | // 	FILE *stream = fopen(argv[optind], "r");
 90 | // 	if (stream == NULL) {
 91 | // 		fprintf(stderr, "Failed open input file list!\n");
 92 | // 		exit(1);
 93 | // 	}
 94 | 
 95 | // 	int file_i = 0, file_m = 1024;
 96 | // 	char **files = malloc(file_m * sizeof(char *));
 97 | 
 98 | // 	char *line = NULL;
 99 | // 	size_t len = 0;
100 | // 	ssize_t nread;
101 | // 	while((nread = getline(&line, &len, stream)) != -1) {
102 | // 		if (nread != 1 && line[0] != '#') {
103 | // 			line[strlen(line) - 1] = '\0';
104 | // 			if (line[0] == '/'){
105 | // 				files[file_i++] = strdup(line);
106 | // 			}else{
107 | // 				char file_path[1024];
108 | // 				sprintf(file_path, "%s/%s", path, line);
109 | // 				files[file_i++] = strdup(file_path);
110 | // 			}
111 | // 			if (file_i >= file_m){
112 | // 				file_m += 1024;
113 | // 				files = realloc(files, file_m * sizeof(char *));
114 | // 			}
115 | // 		}
116 | // 	}
117 | // 	if (line) free(line);
118 | // 	free (path);
119 | // 	fclose(stream);
120 | 
121 | // 	printf("cal_minlen_from_idx: %u file_i %d\n", cal_minlen_from_idx(files, file_i, 18300000), file_i);
122 | // 	for (file_m = 0; file_m < file_i; file_m ++) free (files[file_m]);
123 | // 	free (files);
124 | // 	return 0;
125 | // }
126 | 


--------------------------------------------------------------------------------
/minimap2/LICENSE.txt:
--------------------------------------------------------------------------------
 1 | The MIT License
 2 | 
 3 | Copyright (c) 2018-     Dana-Farber Cancer Institute
 4 |               2017-2018 Broad Institute, Inc.
 5 | 
 6 | Permission is hereby granted, free of charge, to any person obtaining
 7 | a copy of this software and associated documentation files (the
 8 | "Software"), to deal in the Software without restriction, including
 9 | without limitation the rights to use, copy, modify, merge, publish,
10 | distribute, sublicense, and/or sell copies of the Software, and to
11 | permit persons to whom the Software is furnished to do so, subject to
12 | the following conditions:
13 | 
14 | The above copyright notice and this permission notice shall be
15 | included in all copies or substantial portions of the Software.
16 | 
17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
18 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
19 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
20 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
21 | BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
22 | ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
23 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
24 | SOFTWARE.
25 | 


--------------------------------------------------------------------------------
/minimap2/MANIFEST.in:
--------------------------------------------------------------------------------
 1 | include *.h
 2 | include Makefile
 3 | include ksw2_dispatch.c
 4 | include main.c
 5 | include README.md
 6 | include sse2neon/emmintrin.h
 7 | include python/mappy.c
 8 | include python/cmappy.h
 9 | include python/cmappy.pxd
10 | include python/mappy.pyx
11 | include python/README.rst
12 | 


--------------------------------------------------------------------------------
/minimap2/bseq.h:
--------------------------------------------------------------------------------
 1 | #ifndef MM_BSEQ_H
 2 | #define MM_BSEQ_H
 3 | 
 4 | #include <stdint.h>
 5 | #include <string.h>
 6 | 
 7 | #ifdef __cplusplus
 8 | extern "C" {
 9 | #endif
10 | 
11 | struct mm_bseq_file_s;
12 | typedef struct mm_bseq_file_s mm_bseq_file_t;
13 | 
14 | typedef struct {
15 | 	int l_seq, rid;
16 | 	char *name, *seq, *qual, *comment;
17 | } mm_bseq1_t;
18 | 
19 | mm_bseq_file_t *mm_bseq_open(const char *fn);
20 | void mm_bseq_close(mm_bseq_file_t *fp);
21 | mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int with_comment, int frag_mode, int *n_);
22 | mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int frag_mode, int *n_);
23 | mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_);
24 | mm_bseq1_t *mm_bseq_read_frag2(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int with_comment, int *n_);
25 | mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int *n_);
26 | int mm_bseq_eof(mm_bseq_file_t *fp);
27 | 
28 | void set_minlen_nextdenovo(mm_bseq_file_t **fp, const int n_fp, const unsigned minlen);
29 | 
30 | extern unsigned char seq_nt4_table[256];
31 | extern unsigned char seq_comp_table[256];
32 | 
33 | static inline int mm_qname_len(const char *s)
34 | {
35 | 	int l;
36 | 	l = strlen(s);
37 | 	return l >= 3 && s[l-1] >= '0' && s[l-1] <= '9' && s[l-2] == '/'? l - 2 : l;
38 | }
39 | 
40 | static inline int mm_qname_same(const char *s1, const char *s2)
41 | {
42 | 	int l1, l2;
43 | 	l1 = mm_qname_len(s1);
44 | 	l2 = mm_qname_len(s2);
45 | 	return (l1 == l2 && strncmp(s1, s2, l1) == 0);
46 | }
47 | 
48 | static inline void mm_revcomp_bseq(mm_bseq1_t *s)
49 | {
50 | 	int i, t, l = s->l_seq;
51 | 	for (i = 0; i < l>>1; ++i) {
52 | 		t = s->seq[l - i - 1];
53 | 		s->seq[l - i - 1] = seq_comp_table[(uint8_t)s->seq[i]];
54 | 		s->seq[i] = seq_comp_table[t];
55 | 	}
56 | 	if (l&1) s->seq[l>>1] = seq_comp_table[(uint8_t)s->seq[l>>1]];
57 | 	if (s->qual)
58 | 		for (i = 0; i < l>>1; ++i)
59 | 			t = s->qual[l - i - 1], s->qual[l - i - 1] = s->qual[i], s->qual[i] = t;
60 | }
61 | 
62 | #ifdef __cplusplus
63 | }
64 | #endif
65 | 
66 | #endif
67 | 


--------------------------------------------------------------------------------
/minimap2/esterr.c:
--------------------------------------------------------------------------------
 1 | #include <math.h>
 2 | #include <stdio.h>
 3 | #include <stdlib.h>
 4 | #include <assert.h>
 5 | #include "mmpriv.h"
 6 | 
 7 | static inline int32_t get_for_qpos(int32_t qlen, const mm128_t *a)
 8 | {
 9 | 	int32_t x = (int32_t)a->y;
10 | 	int32_t q_span = a->y>>32 & 0xff;
11 | 	if (a->x>>63)
12 | 		x = qlen - 1 - (x + 1 - q_span); // revert the position to the forward strand of query
13 | 	return x;
14 | }
15 | 
16 | static int get_mini_idx(int qlen, const mm128_t *a, int32_t n, const uint64_t *mini_pos)
17 | {
18 | 	int32_t x, L = 0, R = n - 1;
19 | 	x = get_for_qpos(qlen, a);
20 | 	while (L <= R) { // binary search
21 | 		int32_t m = ((uint64_t)L + R) >> 1;
22 | 		int32_t y = (int32_t)mini_pos[m];
23 | 		if (y < x) L = m + 1;
24 | 		else if (y > x) R = m - 1;
25 | 		else return m;
26 | 	}
27 | 	return -1;
28 | }
29 | 
30 | void mm_est_err(const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, const mm128_t *a, int32_t n, const uint64_t *mini_pos)
31 | {
32 | 	int i;
33 | 	uint64_t sum_k = 0;
34 | 	float avg_k;
35 | 
36 | 	if (n == 0) return;
37 | 	for (i = 0; i < n; ++i)
38 | 		sum_k += mini_pos[i] >> 32 & 0xff;
39 | 	avg_k = (float)sum_k / n;
40 | 
41 | 	for (i = 0; i < n_regs; ++i) {
42 | 		mm_reg1_t *r = &regs[i];
43 | 		int32_t st, en, j, k, n_match, n_tot, l_ref;
44 | 		r->div = -1.0f;
45 | 		if (r->cnt == 0) continue;
46 | 		st = en = get_mini_idx(qlen, r->rev? &a[r->as + r->cnt - 1] : &a[r->as], n, mini_pos);
47 | 		if (st < 0) {
48 | 			if (mm_verbose >= 2)
49 | 				fprintf(stderr, "[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.\n");
50 | 			continue;
51 | 		}
52 | 		l_ref = mi->seq[r->rid].len;
53 | 		for (k = 1, j = st + 1, n_match = 1; j < n && k < r->cnt; ++j) {
54 | 			int32_t x;
55 | 			x = get_for_qpos(qlen, r->rev? &a[r->as + r->cnt - 1 - k] : &a[r->as + k]);
56 | 			if (x == (int32_t)mini_pos[j])
57 | 				++k, en = j, ++n_match;
58 | 		}
59 | 		n_tot = en - st + 1;
60 | 		if (r->qs > avg_k && r->rs > avg_k) ++n_tot;
61 | 		if (qlen - r->qs > avg_k && l_ref - r->re > avg_k) ++n_tot;
62 | 		r->div = logf((float)n_tot / n_match) / avg_k;
63 | 	}
64 | }
65 | 


--------------------------------------------------------------------------------
/minimap2/example.c:
--------------------------------------------------------------------------------
 1 | // To compile:
 2 | //   gcc -g -O2 example.c libminimap2.a -lz
 3 | 
 4 | #include <stdlib.h>
 5 | #include <assert.h>
 6 | #include <stdio.h>
 7 | #include <zlib.h>
 8 | #include "minimap.h"
 9 | #include "kseq.h"
10 | KSEQ_INIT(gzFile, gzread)
11 | 
12 | int main(int argc, char *argv[])
13 | {
14 | 	mm_idxopt_t iopt;
15 | 	mm_mapopt_t mopt;
16 | 	int n_threads = 3;
17 | 
18 | 	mm_verbose = 2; // disable message output to stderr
19 | 	mm_set_opt(0, &iopt, &mopt);
20 | 	mopt.flag |= MM_F_CIGAR; // perform alignment
21 | 
22 | 	if (argc < 3) {
23 | 		fprintf(stderr, "Usage: minimap2-lite <target.fa> <query.fa>\n");
24 | 		return 1;
25 | 	}
26 | 
27 | 	// open query file for reading; you may use your favorite FASTA/Q parser
28 | 	gzFile f = gzopen(argv[2], "r");
29 | 	assert(f);
30 | 	kseq_t *ks = kseq_init(f);
31 | 
32 | 	// open index reader
33 | 	mm_idx_reader_t *r = mm_idx_reader_open(argv[1], &iopt, 0);
34 | 	mm_idx_t *mi;
35 | 	while ((mi = mm_idx_reader_read(r, n_threads)) != 0) { // traverse each part of the index
36 | 		mm_mapopt_update(&mopt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
37 | 		mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
38 | 		while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
39 | 			mm_reg1_t *reg;
40 | 			int j, i, n_reg;
41 | 			reg = mm_map(mi, ks->seq.l, ks->seq.s, &n_reg, tbuf, &mopt, 0); // get all hits for the query
42 | 			for (j = 0; j < n_reg; ++j) { // traverse hits and print them out
43 | 				mm_reg1_t *r = &reg[j];
44 | 				assert(r->p); // with MM_F_CIGAR, this should not be NULL
45 | 				printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
46 | 				printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re, r->mlen, r->blen, r->mapq);
47 | 				for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
48 | 					printf("%d%c", r->p->cigar[i]>>4, "MIDNSH"[r->p->cigar[i]&0xf]);
49 | 				putchar('\n');
50 | 				free(r->p);
51 | 			}
52 | 			free(reg);
53 | 		}
54 | 		mm_tbuf_destroy(tbuf);
55 | 		mm_idx_destroy(mi);
56 | 	}
57 | 	mm_idx_reader_close(r); // close the index reader
58 | 	kseq_destroy(ks); // close the query file
59 | 	gzclose(f);
60 | 	return 0;
61 | }
62 | 


--------------------------------------------------------------------------------
/minimap2/kalloc.h:
--------------------------------------------------------------------------------
 1 | #ifndef _KALLOC_H_
 2 | #define _KALLOC_H_
 3 | 
 4 | #include <stddef.h> /* for size_t */
 5 | 
 6 | #ifdef __cplusplus
 7 | extern "C" {
 8 | #endif
 9 | 
10 | typedef struct {
11 | 	size_t capacity, available, n_blocks, n_cores, largest;
12 | } km_stat_t;
13 | 
14 | void *kmalloc(void *km, size_t size);
15 | void *krealloc(void *km, void *ptr, size_t size);
16 | void *kcalloc(void *km, size_t count, size_t size);
17 | void kfree(void *km, void *ptr);
18 | 
19 | void *km_init(void);
20 | void km_destroy(void *km);
21 | void km_stat(const void *_km, km_stat_t *s);
22 | 
23 | #ifdef __cplusplus
24 | }
25 | #endif
26 | 
27 | #endif
28 | 


--------------------------------------------------------------------------------
/minimap2/kthread.h:
--------------------------------------------------------------------------------
 1 | #ifndef KTHREAD_H
 2 | #define KTHREAD_H
 3 | 
 4 | #ifdef __cplusplus
 5 | extern "C" {
 6 | #endif
 7 | 
 8 | void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
 9 | void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_data, int n_steps);
10 | 
11 | #ifdef __cplusplus
12 | }
13 | #endif
14 | 
15 | #endif
16 | 


--------------------------------------------------------------------------------
/minimap2/kvec.h:
--------------------------------------------------------------------------------
  1 | /* The MIT License
  2 | 
  3 |    Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>
  4 | 
  5 |    Permission is hereby granted, free of charge, to any person obtaining
  6 |    a copy of this software and associated documentation files (the
  7 |    "Software"), to deal in the Software without restriction, including
  8 |    without limitation the rights to use, copy, modify, merge, publish,
  9 |    distribute, sublicense, and/or sell copies of the Software, and to
 10 |    permit persons to whom the Software is furnished to do so, subject to
 11 |    the following conditions:
 12 | 
 13 |    The above copyright notice and this permission notice shall be
 14 |    included in all copies or substantial portions of the Software.
 15 | 
 16 |    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 17 |    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 18 |    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 19 |    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
 20 |    BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
 21 |    ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 22 |    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 23 |    SOFTWARE.
 24 | */
 25 | 
 26 | /*
 27 |   An example:
 28 | 
 29 | #include "kvec.h"
 30 | int main() {
 31 | 	kvec_t(int) array;
 32 | 	kv_init(array);
 33 | 	kv_push(int, array, 10); // append
 34 | 	kv_a(int, array, 20) = 5; // dynamic
 35 | 	kv_A(array, 20) = 4; // static
 36 | 	kv_destroy(array);
 37 | 	return 0;
 38 | }
 39 | */
 40 | 
 41 | /*
 42 |   2008-09-22 (0.1.0):
 43 | 
 44 | 	* The initial version.
 45 | 
 46 | */
 47 | 
 48 | #ifndef AC_KVEC_H
 49 | #define AC_KVEC_H
 50 | 
 51 | #include <stdlib.h>
 52 | #include "kalloc.h"
 53 | 
 54 | #define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 55 | 
 56 | #define kvec_t(type) struct { size_t n, m; type *a; }
 57 | #define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
 58 | #define kv_destroy(v) free((v).a)
 59 | #define kv_A(v, i) ((v).a[(i)])
 60 | #define kv_pop(v) ((v).a[--(v).n])
 61 | #define kv_size(v) ((v).n)
 62 | #define kv_max(v) ((v).m)
 63 | 
 64 | #define kv_resize(type, km, v, s) do { \
 65 | 		if ((v).m < (s)) { \
 66 | 			(v).m = (s); \
 67 | 			kv_roundup32((v).m); \
 68 | 			(v).a = (type*)krealloc((km), (v).a, sizeof(type) * (v).m); \
 69 | 		} \
 70 | 	} while (0)
 71 | 
 72 | #define kv_copy(type, km, v1, v0) do { \
 73 | 		if ((v1).m < (v0).n) kv_resize(type, (km), (v1), (v0).n); \
 74 | 		(v1).n = (v0).n; \
 75 | 		memcpy((v1).a, (v0).a, sizeof(type) * (v0).n); \
 76 | 	} while (0) \
 77 | 
 78 | #define kv_push(type, km, v, x) do { \
 79 | 		if ((v).n == (v).m) { \
 80 | 			(v).m = (v).m? (v).m<<1 : 2; \
 81 | 			(v).a = (type*)krealloc((km), (v).a, sizeof(type) * (v).m); \
 82 | 		} \
 83 | 		(v).a[(v).n++] = (x); \
 84 | 	} while (0)
 85 | 
 86 | #define kv_pushp(type, km, v, p) do { \
 87 | 		if ((v).n == (v).m) { \
 88 | 			(v).m = (v).m? (v).m<<1 : 2; \
 89 | 			(v).a = (type*)krealloc((km), (v).a, sizeof(type) * (v).m); \
 90 | 		} \
 91 | 		*(p) = &(v).a[(v).n++]; \
 92 | 	} while (0)
 93 | 
 94 | #define kv_reverse(type, v, start) do { \
 95 | 		if ((v).m > 0 && (v).n > (start)) { \
 96 | 			size_t __i, __end = (v).n - (start); \
 97 | 			type *__a = (v).a + (start); \
 98 | 			for (__i = 0; __i < __end>>1; ++__i) { \
 99 | 				type __t = __a[__end - 1 - __i]; \
100 | 				__a[__end - 1 - __i] = __a[__i]; __a[__i] = __t; \
101 | 			} \
102 | 		} \
103 | 	} while (0)
104 | 
105 | #endif
106 | 


--------------------------------------------------------------------------------
/minimap2/python/minimap2.py:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env python
 2 | 
 3 | import sys
 4 | import getopt
 5 | import mappy as mp
 6 | 
 7 | def main(argv):
 8 | 	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:c")
 9 | 	if len(args) < 2:
10 | 		print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
11 | 		print("Options:")
12 | 		print("  -x STR      preset: sr, map-pb, map-ont, asm5, asm10 or splice")
13 | 		print("  -n INT      mininum number of minimizers")
14 | 		print("  -m INT      mininum chaining score")
15 | 		print("  -k INT      k-mer length")
16 | 		print("  -w INT      minimizer window length")
17 | 		print("  -r INT      band width")
18 | 		print("  -c          output the cs tag")
19 | 		sys.exit(1)
20 | 
21 | 	preset = min_cnt = min_sc = k = w = bw = None
22 | 	out_cs = False
23 | 	for opt, arg in opts:
24 | 		if opt == '-x': preset = arg
25 | 		elif opt == '-n': min_cnt = int(arg)
26 | 		elif opt == '-m': min_chain_score = int(arg)
27 | 		elif opt == '-r': bw = int(arg)
28 | 		elif opt == '-k': k = int(arg)
29 | 		elif opt == '-w': w = int(arg)
30 | 		elif opt == '-c': out_cs = True
31 | 
32 | 	a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
33 | 	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
34 | 	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
35 | 		for h in a.map(seq, cs=out_cs): # traverse hits
36 | 			print('{}\t{}\t{}'.format(name, len(seq), h))
37 | 
38 | if __name__ == "__main__":
39 | 	main(sys.argv)
40 | 


--------------------------------------------------------------------------------
/minimap2/sdust.h:
--------------------------------------------------------------------------------
 1 | #ifndef SDUST_H
 2 | #define SDUST_H
 3 | 
 4 | #include <stdint.h>
 5 | 
 6 | #ifdef __cplusplus
 7 | extern "C" {
 8 | #endif
 9 | 
10 | struct sdust_buf_s;
11 | typedef struct sdust_buf_s sdust_buf_t;
12 | 
13 | // the simple interface
14 | uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n);
15 | 
16 | // the following interface dramatically reduce heap allocations when sdust is frequently called.
17 | sdust_buf_t *sdust_buf_init(void *km);
18 | void sdust_buf_destroy(sdust_buf_t *buf);
19 | const uint64_t *sdust_core(const uint8_t *seq, int l_seq, int T, int W, int *n, sdust_buf_t *buf);
20 | 
21 | #ifdef __cplusplus
22 | }
23 | #endif
24 | 
25 | #endif
26 | 


--------------------------------------------------------------------------------
/minimap2/setup.py:
--------------------------------------------------------------------------------
 1 | try:
 2 | 	from setuptools import setup, Extension
 3 | except ImportError:
 4 | 	from distutils.core import setup
 5 | 	from distutils.extension import Extension
 6 | 
 7 | cmdclass = {}
 8 | 
 9 | try:
10 | 	from Cython.Build import build_ext
11 | except ImportError: # without Cython
12 | 	module_src = 'python/mappy.c'
13 | else: # with Cython
14 | 	module_src = 'python/mappy.pyx'
15 | 	cmdclass['build_ext'] = build_ext
16 | 
17 | import sys, platform
18 | 
19 | sys.path.append('python')
20 | 
21 | extra_compile_args = ['-DHAVE_KALLOC']
22 | include_dirs = ["."]
23 | 
24 | if platform.machine() in ["aarch64", "arm64"]:
25 | 	include_dirs.append("sse2neon/")
26 | 	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
27 | else:
28 | 	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
29 | 
30 | def readme():
31 | 	with open('python/README.rst') as f:
32 | 		return f.read()
33 | 
34 | setup(
35 | 	name = 'mappy',
36 | 	version = '2.17',
37 | 	url = 'https://github.com/lh3/minimap2',
38 | 	description = 'Minimap2 python binding',
39 | 	long_description = readme(),
40 | 	author = 'Heng Li',
41 | 	author_email = 'lh3@me.com',
42 | 	license = 'MIT',
43 | 	keywords = 'sequence-alignment',
44 | 	scripts = ['python/minimap2.py'],
45 |     ext_modules = [Extension('mappy',
46 | 		sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
47 | 				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
48 | 				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
49 | 		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
50 | 				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
51 | 				   'python/cmappy.h', 'python/cmappy.pxd'],
52 | 		extra_compile_args = extra_compile_args,
53 | 		include_dirs = include_dirs,
54 | 		libraries = ['z', 'm', 'pthread'])],
55 | 	classifiers = [
56 | 		'Development Status :: 5 - Production/Stable',
57 | 		'License :: OSI Approved :: MIT License',
58 | 		'Operating System :: POSIX',
59 | 		'Programming Language :: C',
60 | 		'Programming Language :: Cython',
61 | 		'Programming Language :: Python :: 2.7',
62 | 		'Programming Language :: Python :: 3',
63 | 		'Intended Audience :: Science/Research',
64 | 		'Topic :: Scientific/Engineering :: Bio-Informatics'],
65 | 	cmdclass = cmdclass)
66 | 


--------------------------------------------------------------------------------
/minimap2/splitidx.c:
--------------------------------------------------------------------------------
 1 | #include <string.h>
 2 | #include <assert.h>
 3 | #include <stdlib.h>
 4 | #include <stdio.h>
 5 | #include "mmpriv.h"
 6 | 
 7 | FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
 8 | {
 9 | 	char *fn;
10 | 	FILE *fp;
11 | 	uint32_t i, k = mi->k;
12 | 	fn = (char*)calloc(strlen(prefix) + 10, 1);
13 | 	sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
14 | 	if ((fp = fopen(fn, "wb")) == NULL) {
15 | 		if (mm_verbose >= 1)
16 | 			fprintf(stderr, "[ERROR]\033[1;31m failed to write to temporary file '%s'\033[0m\n", fn);
17 | 		exit(1);
18 | 	}
19 | 	mm_err_fwrite(&k, 4, 1, fp);
20 | 	mm_err_fwrite(&mi->n_seq, 4, 1, fp);
21 | 	for (i = 0; i < mi->n_seq; ++i) {
22 | 		uint8_t l;
23 | 		l = strlen(mi->seq[i].name);
24 | 		mm_err_fwrite(&l, 1, 1, fp);
25 | 		mm_err_fwrite(mi->seq[i].name, 1, l, fp);
26 | 		mm_err_fwrite(&mi->seq[i].len, 4, 1, fp);
27 | 	}
28 | 	free(fn);
29 | 	return fp;
30 | }
31 | 
32 | mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part)
33 | {
34 | 	mm_idx_t *mi = 0;
35 | 	char *fn;
36 | 	int i, j;
37 | 
38 | 	if (n_splits < 1) return 0;
39 | 	fn = CALLOC(char, strlen(prefix) + 10);
40 | 	for (i = 0; i < n_splits; ++i) {
41 | 		sprintf(fn, "%s.%.4d.tmp", prefix, i);
42 | 		if ((fp[i] = fopen(fn, "rb")) == 0) {
43 | 			if (mm_verbose >= 1)
44 | 				fprintf(stderr, "ERROR: failed to open temporary file '%s'\n", fn);
45 | 			for (j = 0; j < i; ++j)
46 | 				fclose(fp[j]);
47 | 			free(fn);
48 | 			return 0;
49 | 		}
50 | 	}
51 | 	free(fn);
52 | 
53 | 	mi = CALLOC(mm_idx_t, 1);
54 | 	for (i = 0; i < n_splits; ++i) {
55 | 		mm_err_fread(&mi->k, 4, 1, fp[i]); // TODO: check if k is all the same
56 | 		mm_err_fread(&n_seq_part[i], 4, 1, fp[i]);
57 | 		mi->n_seq += n_seq_part[i];
58 | 	}
59 | 	mi->seq = CALLOC(mm_idx_seq_t, mi->n_seq);
60 | 	for (i = j = 0; i < n_splits; ++i) {
61 | 		uint32_t k;
62 | 		for (k = 0; k < n_seq_part[i]; ++k, ++j) {
63 | 			uint8_t l;
64 | 			mm_err_fread(&l, 1, 1, fp[i]);
65 | 			mi->seq[j].name = (char*)calloc(l + 1, 1);
66 | 			mm_err_fread(mi->seq[j].name, 1, l, fp[i]);
67 | 			mm_err_fread(&mi->seq[j].len, 4, 1, fp[i]);
68 | 		}
69 | 	}
70 | 	return mi;
71 | }
72 | 
73 | void mm_split_rm_tmp(const char *prefix, int n_splits)
74 | {
75 | 	int i;
76 | 	char *fn;
77 | 	fn = CALLOC(char, strlen(prefix) + 10);
78 | 	for (i = 0; i < n_splits; ++i) {
79 | 		sprintf(fn, "%s.%.4d.tmp", prefix, i);
80 | 		remove(fn);
81 | 	}
82 | 	free(fn);
83 | }
84 | 


--------------------------------------------------------------------------------
/minimap2/test/q2.fa:
--------------------------------------------------------------------------------
1 | >q2
2 | GGACATCCCGATGGTGCAGTCCTACCTGTACGAAAGGAC
3 | 


--------------------------------------------------------------------------------
/minimap2/test/t2.fa:
--------------------------------------------------------------------------------
1 | >t2
2 | GGACATCCCGATGGTGCAGgtGCTATTAAAGGTTCGTTTGTTCAACGATTAAagTCCTACCTGTACGAAAGGAC
3 | 


--------------------------------------------------------------------------------
/test_data/input.fofn:
--------------------------------------------------------------------------------
1 | ./reads_test.fa.gz
2 | 


--------------------------------------------------------------------------------
/test_data/reads_test.fa.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/Nextomics/NextDenovo/0e5fa5dae1d0afa33846ff8ad87287ccbe5a1146/test_data/reads_test.fa.gz


--------------------------------------------------------------------------------
/test_data/run.cfg:
--------------------------------------------------------------------------------
 1 | [General]
 2 | job_type = local
 3 | job_prefix = nextDenovo
 4 | task = all # 'all', 'correct', 'assemble'
 5 | rewrite = yes # yes/no
 6 | deltmp = yes
 7 | rerun = 3
 8 | parallel_jobs = 2
 9 | input_type = raw
10 | read_type = clr
11 | input_fofn = ./input.fofn
12 | workdir = ./01_rundir
13 | 
14 | [correct_option]
15 | read_cutoff = 1k
16 | genome_size = 308161
17 | pa_correction = 2
18 | sort_options = -m 1g -t 2
19 | minimap2_options_raw =  -t 8
20 | correction_options = -p 15
21 | 
22 | [assemble_option]
23 | minimap2_options_cns =  -t 8
24 | nextgraph_options = -a 1
25 | 


--------------------------------------------------------------------------------
/util/Makefile:
--------------------------------------------------------------------------------
 1 | CC = gcc
 2 | CFLAGS = -Wall -O3 -Wno-unused-function 
 3 | INCLUDES =
 4 | PROGS = seq_dump ovl_sort seq_stat ovl_cvt seq_bit bam_sort nextgraph
 5 | HTSDIR = ../lib/htslib/
 6 | NEXTGRPHDIR = ./ng
 7 | 
 8 | all:$(PROGS)
 9 | 
10 | $(HTSDIR)/libhts.a:
11 | 	cd  $(HTSDIR) && ./configure --disable-bz2 --disable-lzma
12 | 	@+make -C $(HTSDIR) CPPFLAGS+=-fPIC $(INCLUDES)
13 | 
14 | seq_dump: seq_dump.c ../lib/bseq.c
15 | 	$(CC) $(CFLAGS) $(INCLUDES) -o $@ $^ -lz
16 | 
17 | ovl_sort: ovl_sort.c thpool.c ../lib/ovl.c
18 | 	$(CC) $(CFLAGS) -std=c99 -pthread $(INCLUDES) -o $@ $^
19 | 
20 | ovl_cvt: ovl_cvt.c ../lib/ovl.c
21 | 	$(CC) $(CFLAGS) $(INCLUDES) -o $@ $^
22 | 
23 | seq_bit: seq_bit.c ../lib/bseq.c
24 | 	$(CC) $(CFLAGS) $(INCLUDES) -o $@ $^ -lz
25 | 
26 | seq_stat: seq_stat.c
27 | 	$(CC) $(CFLAGS) -std=c99 $(INCLUDES) -o $@ $^ -lz
28 | 
29 | bam_sort: bam_sort.c ../lib/bsort.c $(HTSDIR)/libhts.a
30 | 	$(CC) $(CFLAGS) -o $@ $^ -I $(HTSDIR) $(INCLUDES) -lpthread -lcurl -lm -lz -lcrypto
31 | 
32 | # align: realign.c ../lib/ovl.c ../lib/bseq.c ../lib/align.c
33 | # 	$(CC) $(CFLAGS) -Wno-unused-function -o $@ $^ -lz
34 | 
35 | nextgraph:
36 | 	make -C $(NEXTGRPHDIR)
37 | 	@+cp $(NEXTGRPHDIR)/$@ ./
38 | 
39 | clean:
40 | 	rm -f *.o $(PROGS)
41 | 	make clean -C $(NEXTGRPHDIR)
42 | 	@+make clean -C $(HTSDIR)
43 | 


--------------------------------------------------------------------------------
/util/ng/Makefile:
--------------------------------------------------------------------------------
 1 | CC=			gcc
 2 | #GENOME_SIZE=0, 1, 2 for small, middle, large genome size
 3 | CPPFLAGS=   -DGENOME_SIZE=0
 4 | CFLAGS=		-Wall -O3  -Wno-unused-function $(CPPFLAGS)
 5 | INCLUDES=
 6 | OBJS=		asg.o ctg.o edge.o kit.o main.o node.o opt.o out.o
 7 | PROG=		nextgraph
 8 | LIBS=		../../lib/bseq.c ../../lib/index.c ../../lib/ovl.c -lm -lz
 9 | 
10 | .SUFFIXES:.c .o
11 | 
12 | .c.o:
13 | 	$(CC) -c $(CFLAGS) -I. $(INCLUDES) $< -o $@
14 | 
15 | all:$(PROG)
16 | 
17 | nextgraph:$(OBJS) main.o
18 | 	$(CC) $(CFLAGS) $^ $(INCLUDES) -o $@ $(LIBS)
19 | clean:
20 | 	rm -fr *.o a.out $(PROG) *~
21 | 


--------------------------------------------------------------------------------
/util/ng/asg.h:
--------------------------------------------------------------------------------
 1 | #ifndef _ASG_H_
 2 | #define _ASG_H_
 3 | #include "common.h"
 4 | #include "node.h"
 5 | #include "edge.h"
 6 | #include "opt.h"
 7 | 
 8 | void init_graph(graph *s, const uint32_t len);
 9 | void destroy_graph(graph *s);
10 | void rm_node_con(graph *g, khash_t(ovlinfo_) *os, opt *p, list *l);
11 | void sort_stat_oe(graph *g, det *d, opt *p);
12 | void rm_edge_lq(graph *g, khash_t(ovlinfo_) *os, opt *p, list *l);
13 | void rm_edge_chim(graph * g, const int s, const float sco, const uint32_t ide, const uint16_t l);
14 | void rm_edge_ltc(graph *g, const int s, const float sco, const float idt, const int l);
15 | void calc_edge_tc(graph *g, const int s);
16 | void mark_edge_rep(graph *g, khash_t(ovlinfo_) *os, opt *p, const det *d, list *l);
17 | void mark_edge_tr(graph *g, const int fuzz);
18 | void rm_edge_spur(graph *g);
19 | void mark_edge_hli(graph *g, const float max_ide_ratio);
20 | void rm_edge_li(graph *g);
21 | void mark_edge_hls(graph *g, const float max_sco_ratio);
22 | void mark_node_chim(graph *g, const int s, const int m, const int md, int *kc);
23 | //void mark_node_chim(graph *g);
24 | void rm_edge_ls(graph *g);
25 | void mark_edge_bs(graph *g);
26 | void rm_sht_brh(graph *g, const int s, const int l);
27 | void rm_z_clip_lable(graph *g, const int s, const int m, const uint16_t l);
28 | void cal_node_io_bstsc(graph *g, const int s);
29 | void rm_z_clip_score(graph *g, const int s, const int m);
30 | void rm_sht_loop(graph *g, const int s);
31 | void rm_sht_bubble(graph *g, const int s);
32 | void rm_end_loop(graph *g, const int s);
33 | void clean_complex_path(graph *g, const int s, const int r, const uint16_t l);
34 | void update_graph(char *file, graph *g, khash_t(ovlinfo_) *os, opt *p, uint32_t *arr, list *l);
35 | 
36 | 
37 | void clean_complex_single_path(graph *g, const int s, const int m, const float perc);
38 | void clean_complex_multi_path(graph *g, const int s, const int m, const float perc);
39 | void rm_z_clip_score3(graph *g, const int s, const int m, const int perc);
40 | void clean_complex_graph(graph *g, const int s, const int m, const float perc);
41 | void rm_z_clip_score2(graph *g, const int s, const int m, const int perc);
42 | void rm_long_bubble(graph *g, const int s, const int m, const float perc);
43 | #endif
44 | 


--------------------------------------------------------------------------------
/util/ng/common.h:
--------------------------------------------------------------------------------
 1 | #ifndef _COM_H_
 2 | #define _COM_H_
 3 | #include <stdint.h>
 4 | #include "kit.h"
 5 | 
 6 | typedef struct node_ {// size 32
 7 | 	UINT_T l; // lable, >= 2 bit
 8 | 	UINT_T id; // in degree
 9 | 	UINT_T idm; // max in degree
10 | 	UINT_T od; // out degree
11 | 	UINT_T odm; // max out degree
12 | 	UINTL_T name; // node name
13 | 	UINTL_T *ie; // index of in edge
14 | 	UINTL_T *oe; // index of out edge
15 | } node;
16 | 
17 | typedef struct edge_ {//size 24
18 | 	uint16_t l; // lable
19 | 	uint16_t ide; // aln identity
20 | 	UINTL_T in; // index of in node
21 | 	UINTL_T ou; // index of out node
22 | 	uint32_t tc:8; // triangle count
23 | 	uint32_t ie:24; // in end
24 | 	uint32_t oe; // out end
25 | 	uint32_t len; // edge length
26 | 	uint32_t sco; // aln length
27 | } edge;
28 | 
29 | typedef struct graph_ {
30 | 	node *nd; // node
31 | 	edge *eg; // edge
32 | 	UINTL_T ni; // node index
33 | 	UINTL_T nm; // node max
34 | 	UINTL_T ei; // edge index
35 | 	UINTL_T em; // edge max
36 | } graph;
37 | 
38 | #endif
39 | 


--------------------------------------------------------------------------------
/util/ng/ctg.h:
--------------------------------------------------------------------------------
 1 | #ifndef _CTG_H_
 2 | #define _CTG_H_
 3 | #include "common.h"
 4 | 
 5 | typedef struct {
 6 | 	uint32_t lq:2;
 7 | 	uint32_t ide:10; // identity
 8 | 	uint32_t ort:10; // matched out_len/Max ratio
 9 | 	uint32_t irt:10; // matched in_len/Max ratio
10 | 	uint32_t l; // strand, 0=+, 1=-
11 | 	uint32_t s; // start, UINT32_MAX == reads end
12 | 	uint32_t e; // end
13 | 	UINTL_T name; // reads name
14 | 	UINTL_T nidex; // node index
15 | } ctg__;
16 | 
17 | typedef struct {
18 | 	ctg__ *nd;
19 | 	// 0:unknown; 1:linear; 2:loop; 3:od==0; 4:id>1 && od>1;
20 | 	// {"unknown", "linear", "loop", "breakpoint", "junction"}
21 | 	uint32_t type; 
22 | 	uint32_t len;
23 | 	uint32_t i;
24 | 	uint32_t im;
25 | } ctg_;
26 | 
27 | typedef struct {
28 | 	ctg_ *ctg;
29 | 	uint32_t i;
30 | 	uint32_t im;
31 | } ctgs;
32 | 
33 | void init_ctgs(ctgs *s, const uint32_t len);
34 | void destroy_ctgs(ctgs *s);
35 | void generate_ctg(graph *g, ctgs *s, const uint16_t l);
36 | 
37 | #endif
38 | 


--------------------------------------------------------------------------------
/util/ng/edge.h:
--------------------------------------------------------------------------------
 1 | #ifndef _EDGE_H_
 2 | #define _EDGE_H_
 3 | #include "common.h"
 4 | #include "opt.h"
 5 | #include "../../lib/ovl.h"
 6 | 
 7 | #define MFLAG_FIT	0x1
 8 | #define MFLAG_REP1	0x2
 9 | #define MFLAG_REP2	0x4
10 | #define MFLAG_TR	0x8
11 | #define MFLAG_LS	0x10
12 | #define MFLAG_HS	0x20
13 | #define MFLAG_BS	0x40
14 | #define MFLAG_CN	0x80
15 | #define MFLAG_CC	0x100
16 | #define MFLAG_LQ	0x200
17 | #define MFLAG_HI	0x400
18 | #define MFLAG_LI	0x800
19 | 
20 | #define MFLAG_IL	0x2000
21 | #define MFLAG_OL	0x4000
22 | #define MFLAG_TT	0x8000 //temp flag
23 | 
24 | void reallocate_edge(graph *s, const uint32_t len);
25 | int check_valid_edge(edge *e, opt *p, ovlinfo *loli, ovlinfo *roli); //TODO: del contained edge
26 | uint32_t check_exited_edge(graph *g, const UINTL_T in, const UINTL_T ou);// only used in update_graph
27 | UINTL_T rp_exited_edge(graph *g, const UINTL_T in, const UINTL_T ou);// replace existed edge
28 | UINTL_T get_reversed_edge(graph *g, const UINTL_T n);
29 | UINTL_T get_edge(graph *g, const UINTL_T in, const UINTL_T ou);
30 | uint32_t get_oreadlen(graph *g, UINTL_T n);
31 | uint32_t get_ireadlen(graph *g, UINTL_T n);
32 | UINTL_T stat_valid_edge(graph *g);
33 | /*uint32_t add_edge(graph *g, const uint32_t in, const uint32_t ou, const uint32_t ie,\
34 | 	const uint32_t oe, const uint32_t sco, const uint16_t ide, const uint32_t len, const uint32_t l);
35 | void rm_edge(graph *g, const uint32_t n);*/
36 | 
37 | #endif
38 | 


--------------------------------------------------------------------------------
/util/ng/kit.c:
--------------------------------------------------------------------------------
 1 | #include <stdio.h>
 2 | #include <stdlib.h>
 3 | #include <time.h>
 4 | #include <stdarg.h>
 5 | #include <sys/time.h>
 6 | #include <sys/resource.h>
 7 | #include "kit.h"
 8 | 
 9 | //from minimap2
10 | double cputime()
11 | {
12 |     struct rusage r;
13 |     getrusage(RUSAGE_SELF, &r);
14 |     return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
15 | }
16 | 
17 | long peakrss()
18 | {
19 |     struct rusage r;
20 |     getrusage(RUSAGE_SELF, &r);
21 | #ifdef __linux__
22 |     return r.ru_maxrss * 1024;
23 | #else
24 |     return r.ru_maxrss;
25 | #endif
26 | }
27 | 
28 | double realtime()
29 | {
30 |     struct timeval tp; 
31 |     gettimeofday(&tp, NULL);
32 |     return tp.tv_sec + tp.tv_usec * 1e-6;
33 | }
34 | 
35 | 
36 | void plog(const int level, char *format, ...)
37 | {	
38 |     char *type[5] = {"NOTSET", "DEBUG", "INFO", "WARNING", "ERROR"};
39 |     time_t t;
40 |     struct tm *lt;
41 |     time(&t);
42 |     lt = localtime(&t);
43 | 
44 |     va_list ap; 
45 |     va_start(ap, format);
46 |     fprintf(stderr, "[%s] %02d-%02d-%02d %02d:%02d:%02d ", type[level], \
47 |     lt->tm_year+1900, lt->tm_mon+1, lt->tm_mday, lt->tm_hour, \
48 |     lt->tm_min, lt->tm_sec);
49 |     vfprintf(stderr, format, ap);
50 |     va_end(ap);
51 |     fprintf(stderr, "\n");
52 | }
53 | 
54 | void init_sn(ph *s, const int len){
55 |     s->im = len;
56 |     s->i = 0;
57 |     s->n = malloc(s->im * sizeof(UINTL_T));
58 | }
59 | 
60 | void reallocate_sn(ph *s, const int len){
61 |     s->im += len;
62 |     s->n = realloc(s->n, sizeof(UINTL_T) * s->im);
63 | }
64 | 
65 | void destroy_sn(ph *s){
66 |     free (s->n);
67 | }
68 | 
69 | int version(){
70 |     fprintf(stderr, "TYPE_GS: %d, UINT_T: %lu, UINTL_T: %lu, ",\
71 |         GENOME_SIZE, sizeof(UINT_T) * 8, sizeof(UINTL_T) * 8);
72 |     #ifdef RESTRICT
73 |         fprintf(stderr, "RESTRICT_GS: %lu\n", RESTRICT_GS);
74 |     #else
75 |         fprintf(stderr, "RESTRICT_GS: NA\n");
76 |     #endif
77 |     return 1;
78 | }
79 | 
80 | int quick_select(int *r, int s, int e, int k){
81 |     if (s > e) return e + 1;
82 |     int i, left, pivot;
83 |     while (1){
84 |         left = s;
85 |         pivot = r[e];
86 |         for (i = s; i < e; i++){
87 |             if(r[i] < pivot){
88 |                 SWAP(r[i], r[left], int);
89 |                 left++;
90 |             }
91 |         }
92 |         SWAP(r[left], r[e], int);
93 | 
94 |         if (left == k) return pivot;
95 |         if (left < k) s = left + 1;
96 |         else e = left - 1;
97 |     }
98 | }


--------------------------------------------------------------------------------
/util/ng/kit.h:
--------------------------------------------------------------------------------
 1 | #ifndef _KIT_H_
 2 | #define _KIT_H_
 3 | #include <inttypes.h>
 4 | 
 5 | // #define GENOME_SIZE 1
 6 | 
 7 | #if GENOME_SIZE == 1
 8 | 	#define UINT_T uint32_t
 9 | 	#define UINT_FORMAT PRIu32
10 | 	#define UINTL_T uint32_t
11 | 	#define UINTL_FORMAT PRIu32
12 | #elif GENOME_SIZE == 2
13 | 	#define UINT_T uint32_t
14 | 	#define UINT_FORMAT PRIu32
15 | 	#define UINTL_T uint64_t
16 | 	#define UINTL_FORMAT PRIu64
17 | #else
18 | 	#define UINT_T uint16_t
19 | 	#define UINT_FORMAT PRIu16
20 | 	#define UINTL_T uint32_t
21 | 	#define UINTL_FORMAT PRIu32
22 | #endif
23 | 
24 | #define MAX_INIT_N 65536
25 | #define RANDOM_COUNT 10000000
26 | #define SWAP(x, y, T) do { T SWAP = x; x = y; y = SWAP; } while (0)
27 | 
28 | //#define RESTRICT
29 | #define RESTRICT_GS 3500000000L
30 | 
31 | //#define P_VERSION
32 | 
33 | typedef struct {
34 | 	UINTL_T *n;
35 | 	int64_t i;
36 | 	int64_t im;
37 | } ph;
38 | 
39 | typedef struct {
40 | 	//uint64_t d[2]; // raw depth, dovetail depth
41 | 	UINTL_T l[2]; // low count
42 | 	UINTL_T n[2]; // record count
43 | 	UINTL_T h[2]; // high record count
44 | } det;
45 | 
46 | double cputime();
47 | long peakrss();
48 | double realtime();
49 | void plog(const int level, char *format, ...);
50 | void init_sn(ph *s, const int len);
51 | void reallocate_sn(ph *s, const int len);
52 | void destroy_sn(ph *s);
53 | int version();
54 | int quick_select(int *r, int s, int e, int k);
55 | 
56 | #endif
57 | 


--------------------------------------------------------------------------------
/util/ng/node.h:
--------------------------------------------------------------------------------
 1 | #ifndef _NODE_H_
 2 | #define _NODE_H_
 3 | #include "common.h"
 4 | 
 5 | UINTL_T get_reversed_node(graph *g, const UINTL_T n);
 6 | UINTL_T add_node(graph *g, const UINTL_T name, const int len);
 7 | UINT_T get_validly_oe(graph *g, const UINTL_T n, const UINT_T i);
 8 | UINT_T get_validly_ie(graph *g, const UINTL_T n, const UINT_T i);
 9 | void rm_oe(graph *g, const UINTL_T n, const UINTL_T e);
10 | void rm_ie(graph *g, const UINTL_T n, const UINTL_T e);
11 | void rm_node(graph *g, const UINTL_T n);
12 | int add_oe(graph *g, const UINTL_T n, const UINTL_T e);
13 | int add_ie(graph *g, const UINTL_T n, const UINTL_T e);
14 | void clean_node_lable(graph *g);
15 | UINTL_T stat_valid_node(graph *g);
16 | int check_node_lable(graph *g, const UINTL_T n, const uint16_t l);
17 | 
18 | #endif
19 | 


--------------------------------------------------------------------------------
/util/ng/opt.h:
--------------------------------------------------------------------------------
 1 | #ifndef _OPT_H_
 2 | #define _OPT_H_
 3 | #include <stdint.h>
 4 | #include <stdio.h>
 5 | #include <getopt.h>
 6 | 
 7 | typedef struct opt_ {
 8 | 	FILE *fa; // input seq list, f
 9 | 	// FILE *bl; // input black list, b
10 | 	int out_format;//out_seq; // output assembly sequences, a
11 | 	int debug; //debug mode, d
12 | 	int sort; // sort out edges by len
13 | 	int fuzz_len;//fuzz; // fuzz len for trans-reduction, F
14 | 	int chimera;//pre filter chimeric reads, c
15 | 	int keep_chimera_edge;//retain potential chimeric edges, G
16 | 	int bfs_depth;//ext_node_count;// depth of BFS to identify chimeric nodes, D
17 | 	int bfs_depth_multi;//ext_depth_multi;// max depth multiple of a node for BFS, P
18 | 	int keep_comp_path;// romove all compound path, k
19 | 	int out_spath_len;// min short branch len for output, q
20 | 	// int out_zpath_len;// min z path len for output, Q
21 | 	int refilt_con_read;//disable refilter contained reads, R
22 | 	int min_con_count; // min contained count to filter reads, u
23 | 	int out_ctg_len;// min contig len, E
24 | 	int max_aln_depth; // max aligned depth
25 | 	int min_aln_depth; // min aligned depth
26 | 	int sbranch_len;//short_branch_len; // max len of a short branch, l
27 | 	int zbranch_len; // max len of a z branch, z
28 | 	int sloop_len;//short_loop_len; // max len of a loop, L
29 | 	int bubble_len; // max len of a bubble, B
30 | 	int end_loop_len; // max len of a terminal loop
31 | 	int cpath_len;//comp_path_len; // max len of a compound path, C
32 | 	// int max_gap_len; // max gap len of two path
33 | 	// int max_hang_plen; // max over hang length at two end overlap to identity dovetails
34 | 	int max_hang_len;//max_hang_tlen; // max over hang length at two end overlap of dovetails, t
35 | 	// int thread;// T
36 | 	int min_node_count;//min valid node count of a read, N
37 | 	uint32_t min_ide; // min identity of alignments. i
38 | 	float min_ide_ratio; // min test-to-best identity ratio, I
39 | 	float max_ide_ratio; // max test-to-best identity ratio of a low quality edge, R
40 | 	float min_sco_ratio; // min test-to-best aligned length ratio, S
41 | 	float min_depth_multi; // min depth multiple of a repeat node, m
42 | 	float max_depth_multi; // max depth multiple of a node, n
43 | 	float max_sco_ratio; //min test-to-best score ratio of a node, r
44 | 	int min_edge_cov; //min depth of an edge, w
45 | 	int out_alt_ctg; // output alternative contigs, A
46 | 	float min_mat_ratio; //min test-to-best matches ratio, M
47 | 	float min_depth_ratio;//min_edepth_ratio; //min test-to-best depth ratio of an edge, T
48 | 	int median_aln_depth;
49 | 	int median_outdegree;
50 | } opt;
51 | 
52 | void init_opt(opt *p);
53 | int usage(opt *opts);
54 | 
55 | #endif
56 | 


--------------------------------------------------------------------------------
/util/ng/out.h:
--------------------------------------------------------------------------------
 1 | #ifndef _OUT_H_
 2 | #define _OUT_H_
 3 | #include "common.h"
 4 | #include "ctg.h"
 5 | #include "../../lib/index.h"
 6 | 
 7 | void stat_ctg(ctgs *m, const uint64_t gs);
 8 | void out_node(graph *s, const UINTL_T j);
 9 | uint64_t out_ctg_path(ctgs *m, const idxs *idx, const int min_ctg_len);
10 | uint64_t out_ctg_gfa(ctgs *m, graph *g, const idxs *idx, const int min_ctg_len);//TODO need more test
11 | uint64_t out_ctg_fasta(ctgs *m, const idxs *idx, const int min_ctg_len, const int out_seq);
12 | void out_graph_raw(graph *s);
13 | void out_graph_graphml(graph *s);
14 | void out_edges(graph *g);
15 | 
16 | #endif
17 | 


--------------------------------------------------------------------------------
/util/ovl_cvt.c:
--------------------------------------------------------------------------------
 1 | #include <stdio.h>
 2 | #include <stdlib.h>
 3 | #include <stdint.h>
 4 | #include <unistd.h>
 5 | #include <string.h>
 6 | #include "../lib/ovl.h"
 7 | 
 8 | void encode(FILE *fp, FILE *fq, bytes_t *arr, prev_t *id, int mode)
 9 | {
10 |   buffer_t *buf = init_buffer(ECBUFSIZE);
11 |   char *line = NULL;
12 |   size_t len = 0;
13 |   init_ovl_mode(fq, mode);
14 |   if (mode == 8){
15 |     overlap ovl;
16 |     while(getline(&line, &len, fp) != -1) {
17 |       sscanf(line, "%u\t%hhu\t%u\t%u\t%u\t%u\t%u\t%u\n", &ovl.qname, &ovl.rev,\
18 |         &ovl.qs, &ovl.qe, &ovl.tname, &ovl.ts, &ovl.te, &ovl.match);
19 |       encode_ovl(fq, arr, id, &ovl, buf);
20 |     }
21 |   }else{
22 |     overlap_i ovl;
23 |     while(getline(&line, &len, fp) != -1) {
24 |       sscanf(line, "%u\t%hhu\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", &ovl.qname, &ovl.rev, &ovl.qs, \
25 |         &ovl.qe, &ovl.tname, &ovl.ts, &ovl.te, &ovl.qlen, &ovl.tlen, &ovl.identity);
26 |       encode_ovl_i(fq, arr, id, &ovl, buf);
27 |     }
28 |   }
29 |   flush_buffer(fq, buf);
30 |   if (line) free(line);
31 | }
32 | 
33 | void decode(FILE *fp, FILE *fq, uint32_t *arr, prev_t *id, int mode)
34 | {
35 |   buffer_t *buf = init_buffer(DCBUFSIZE);
36 |   uint32_t ovl[10];
37 |   uint32_t qlen = 0, tlen = 0;
38 |   while(decode_ovl(fp, arr, id, ovl, buf, mode) >= 0) {
39 |     if (mode == 8){
40 |       fprintf(fq, "%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", ovl[0], ovl[1], \
41 |         ovl[2], ovl[3], ovl[4], ovl[5], ovl[6], ovl[7]);
42 |     }else{
43 |       if (ovl[7]) qlen = ovl[7];
44 |       if (ovl[8]) tlen = ovl[8];
45 |       fprintf(fq, "%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", ovl[0], ovl[1], \
46 |         ovl[2], ovl[3], ovl[4], ovl[5], ovl[6], qlen, tlen, ovl[9]);
47 |     }
48 |   }
49 |   flush_buffer(NULL, buf);
50 | }
51 | 
52 | static int usage()
53 | {
54 |   fprintf(stderr, "Usage: ovl_cvt [options] input.ovl\n");
55 |   fprintf(stderr, "Compress or uncompress ovl files\n\n");
56 |   fprintf(stderr, "Options:\n");
57 |   fprintf(stderr, " -m INT    conversion mode (0 for compress, 1 for uncompress)\n");
58 |   return 1;
59 | }
60 | 
61 | int main(int argc, char *argv[])
62 | {
63 |   int c, mode = 0;
64 |   while((c = getopt(argc, argv, "m:")) != -1) {
65 |     switch (c) {
66 |       case 'm':
67 |         mode = atoi(optarg);
68 |         break;
69 |       default:
70 |         return usage();
71 |     }
72 |   }
73 |   if (optind + 1 > argc) return usage();
74 |   FILE *fp;
75 |   fp = mode ? fopen(argv[optind], "rb"): fopen(argv[optind], "r");
76 |   if (fp == NULL) {
77 |     fprintf(stderr, "Failed open input file!\n");
78 |     return usage();
79 |   }
80 |   prev_t id;
81 |   id.prev_qname = id.prev_tname = 0;
82 |   if (mode) {
83 |     uint32_t *arr = init_decode_table(NUM_LIMIT);
84 |     mode = find_ovlb_mode(fp);
85 |     decode(fp, stdout, arr, &id, mode);
86 |     destroy_table(arr);
87 |   } else {
88 |     bytes_t *arr = init_encode_table(NUM_LIMIT);
89 |     mode = find_ovlt_mode(fp);
90 |     encode(fp, stdout, arr, &id, mode);
91 |     destroy_table(arr);
92 |   }
93 |   fclose(fp);
94 |   return 0;
95 | }


--------------------------------------------------------------------------------
/util/ovl_sort.h:
--------------------------------------------------------------------------------
 1 | #include "../lib/ovl.h"
 2 | 
 3 | #define BIN_OFFSET 6
 4 | #define MAX_OVL_COV 150
 5 | #define MAX_READ_THREAD 4
 6 | #define MAX_SORT_THREAD 10
 7 | #define MAX_PATH_LENGTH 1024
 8 | #define MAX_BIN_COUNT 31250 //2m
 9 | #define MIN_MEM_UNIT 100000000
10 | #define BIN_TOLERANCE_EDGE 50
11 | #define BIN_TOLERANCE_COUNT 5
12 | #define MIN_CONTAINTED_COUNT 2
13 | 
14 | typedef struct {
15 | 	char files[MAX_PATH_LENGTH];
16 | 	FILE *fp;
17 | 	buffer_t *buf;
18 | 	prev_t seed_name;
19 | } file;
20 | 
21 | typedef struct {
22 | 	file *files;
23 | 	uint32_t len;
24 | 	uint32_t max_size;
25 | } overlap_file;
26 | 
27 | typedef struct {
28 | 	char *outfile;
29 | 	overlap *ovls;
30 | 	uint8_t sorted;
31 | 	uint8_t saved;
32 | 	uint32_t len;
33 | 	uint32_t max_ovls_len;
34 | 	uint32_t max_size;
35 | } overlap_data;
36 | 
37 | typedef struct {
38 | 	FILE *rp;
39 | 	uint8_t save_seed;
40 | 	char outfile[MAX_PATH_LENGTH];
41 | 	overlap_file *input_file;
42 | 	overlap_data *input_data;
43 | 	threadpool thpool;
44 | 	int input_data_len;
45 | 	int input_file_index;
46 | 	int input_file_step;
47 | } sort_args;
48 | 
49 | typedef struct {
50 | 	int max_thread;
51 | 	int input_data_len;
52 | 	int max_readfile_in_single_thread;
53 | 	uint64_t max_mem_each_file;
54 | } merge_thread_opt;
55 | 
56 | typedef struct {
57 | 	uint8_t pcount;
58 | 	uint16_t ovl_i, ovl_m;
59 | 	uint16_t *bins;
60 | 	overlap *ovls;
61 | 	uint32_t qname, qs, qe, qlen, qmaxlen, qcov;
62 | 	uint32_t binlen, bincount;
63 | 	uint32_t contained, chimera;
64 | 	uint32_t max_size, len;
65 | } cov_data;
66 | 
67 | typedef struct {
68 | 	char *idx;
69 | 	char *outfile;
70 | 	char tempdir[MAX_PATH_LENGTH];
71 | 	int thread;
72 | 	uint64_t max_mem;
73 | } opt;
74 | 
75 | static inline uint64_t mm_parse_num(const char *str);
76 | static int get_inputfile_index(sort_args *sort);
77 | static int get_outputfile_index();
78 | static int get_overlapdata_index(sort_args *sort);
79 | static inline int check_chimer(cov_data *cov);
80 | static inline void out_chi_con(cov_data *cov, FILE *fp);
81 | static inline void encode_ovl_filter(FILE *fp, FILE *rp, prev_t *name, overlap *ovl, cov_data *cov, buffer_t *buf);
82 | 
83 | void init_seeds(char *file);
84 | void sort_ovl(overlap_data *input_data);
85 | void merge_ovl_from_file (sort_args *sort);
86 | void merge_ovl_from_sort(sort_args *sort);
87 | void sort_ovl_file(sort_args *sort);
88 | void print_log(char *format, ...);
89 | void collect_ovl_file(char *file, overlap_file *ovlfiles);
90 | void init_cov(cov_data *cov);
91 | void init_ovlfiles(overlap_file *ovlfiles, char *infile);
92 | void init_mt_opt(merge_thread_opt *mt_opt, opt *opts, int sorted_files_len);
93 | void init_sort(sort_args*, uint8_t, threadpool, overlap_file*, opt*, int, uint64_t, int, int);
94 | void destroy_sort_input(sort_args *sort);
95 | int cmp_ovl(const void *a_, const void *b_);
96 | int load_input_data_from_file(overlap_data *input_data, FILE *fp, buffer_t *buf, prev_t *name);
97 | FILE *init_rp(opt *opts);
98 | 


--------------------------------------------------------------------------------
/util/seq_bit.c:
--------------------------------------------------------------------------------
 1 | #include <stdio.h>
 2 | #include <stdint.h>
 3 | #include "../lib/bseq.h"
 4 | 
 5 | static int usage()
 6 | {
 7 | 	fprintf(stderr, "Usage: seq_bit [options] input.[fa|bit]\n");
 8 | 	fprintf(stderr, "Compress or uncompress fa/bit files, seq name must be number\n\n");
 9 | 	return 1;
10 | }
11 | 
12 | int main(int argc, char *argv[])
13 | {
14 | 	if (optind + 1 > argc) return usage();
15 | 	gzFile fp = gzopen(argv[optind], "r");
16 | 	if (fp == NULL) {
17 | 		fprintf(stderr, "Failed open input file!\n");
18 | 		return usage();
19 | 	}
20 | 	
21 | 	int lable = 1;
22 | 	kseq_t *seq = kseq_init(fp);
23 | 	while ((kseq_r(seq)) >= 0) {
24 | 		if (seq->fm == 1){
25 | 			if (lable) {init_seq_mode(stdout); lable = 0;}
26 | 			seq2bit(stdout, strtoul(seq->name.s, NULL, 10), seq->seq.l, seq->seq.s);
27 | 		}else{
28 | 			printf(">%s\n%s\n", seq->name.s, seq->seq.s);
29 | 		}
30 | 	}
31 | 	kseq_destroy(seq);
32 | 	gzclose(fp);
33 | 	return 0;
34 | }
35 | 


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