├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── README.md ├── annotations ├── ceph18.b37.exclude.2014-01-15.bed ├── ceph18.b37.include.2014-01-15.bed ├── ceph18.b37.lumpy.exclude.2014-01-15.bed ├── exclude.cnvnator_100bp.112015.bed └── exclude.cnvnator_100bp.GRCh38.20170403.bed ├── bin ├── annotate_rd.py ├── cnvnator_wrapper.py ├── speedseq └── speedseq.config ├── etc ├── add_storage-01.png ├── community_ami-01.png ├── instance_type-01.png ├── launch-01.png ├── speedseq-logo.png ├── speedseq-logo.svg └── speedseq_workflow.png ├── example ├── data │ ├── NA12878.20slice.30X.fastq.gz │ ├── human_g1k_v37_20_42220611-42542245.fasta │ ├── human_g1k_v37_20_42220611-42542245.fasta.amb │ ├── human_g1k_v37_20_42220611-42542245.fasta.ann │ ├── human_g1k_v37_20_42220611-42542245.fasta.bwt │ ├── human_g1k_v37_20_42220611-42542245.fasta.fai │ ├── human_g1k_v37_20_42220611-42542245.fasta.pac │ └── human_g1k_v37_20_42220611-42542245.fasta.sa ├── example_speedseq_install.sh └── run_speedseq.sh └── src ├── mbuffer ├── .hg_archival.txt ├── .hgtags ├── AUTHORS ├── ChangeLog ├── INSTALL ├── LICENSE ├── Makefile.in ├── NEWS ├── README ├── config.guess ├── config.h.in ├── config.sub ├── configure ├── configure.in ├── dest.h ├── install-sh ├── log.c ├── log.h ├── mbuffer.1.in ├── mbuffer.c ├── network.c └── network.h ├── sambamba └── samtools-1.3.1 ├── AUTHORS ├── ChangeLog.old ├── INSTALL ├── LICENSE ├── Makefile ├── Makefile.mingw ├── NEWS ├── README ├── aclocal.m4 ├── bam.c ├── bam.h ├── bam2bcf.c ├── bam2bcf.h ├── bam2bcf_indel.c ├── bam2depth.c ├── bam_addrprg.c ├── bam_aux.c ├── bam_cat.c ├── bam_color.c ├── bam_endian.h ├── bam_flags.c ├── bam_import.c ├── bam_index.c ├── bam_lpileup.c ├── bam_lpileup.h ├── bam_mate.c ├── bam_md.c ├── bam_plbuf.c ├── bam_plbuf.h ├── bam_plcmd.c ├── bam_quickcheck.c ├── bam_reheader.c ├── bam_rmdup.c ├── bam_rmdupse.c ├── bam_sort.c ├── bam_split.c ├── bam_stat.c ├── bam_tview.c ├── bam_tview.h ├── bam_tview_curses.c ├── bam_tview_html.c ├── bamshuf.c ├── bamtk.c ├── bedcov.c ├── bedidx.c ├── config.h.in ├── config.mk.in ├── configure ├── configure.ac ├── cut_target.c ├── dict.c ├── errmod.c ├── errmod.h ├── examples ├── 00README.txt ├── ex1.fa ├── toy.fa └── toy.sam ├── faidx.c ├── htslib-1.3.1 ├── INSTALL ├── LICENSE ├── Makefile ├── NEWS ├── README ├── bgzf.c ├── 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 │ ├── thread_pool.c │ ├── thread_pool.h │ ├── vlen.c │ ├── vlen.h │ ├── zfio.c │ └── zfio.h ├── faidx.5 ├── faidx.c ├── hfile.c ├── hfile_internal.h ├── hfile_irods.c ├── hfile_libcurl.c ├── hfile_net.c ├── hts.c ├── hts_internal.h ├── htsfile.1 ├── htsfile.c ├── htslib.mk ├── htslib.pc.in ├── htslib │ ├── bgzf.h │ ├── cram.h │ ├── faidx.h │ ├── hfile.h │ ├── hts.h │ ├── hts_defs.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 │ ├── vcf.h │ ├── vcf_sweep.h │ └── vcfutils.h ├── htslib_vars.mk ├── kfunc.c ├── knetfile.c ├── kstring.c ├── md5.c ├── plugin.c ├── regidx.c ├── sam.5 ├── sam.c ├── synced_bcf_reader.c ├── tabix.1 ├── tabix.c ├── tbx.c ├── test │ ├── aux#aux_java.cram │ ├── auxf#values.sam │ ├── auxf.fa │ ├── auxf.fa.fai │ ├── 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#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 │ ├── fieldarith.c │ ├── fieldarith.sam │ ├── formatcols.vcf │ ├── hfile.c │ ├── noroundtrip-out.vcf │ ├── noroundtrip.vcf │ ├── sam.c │ ├── test-regidx.c │ ├── test-vcf-api.c │ ├── test-vcf-api.out │ ├── test-vcf-hdr-in.vcf │ ├── test-vcf-hdr.out │ ├── test-vcf-sweep.c │ ├── test-vcf-sweep.out │ ├── test.pl │ ├── test_view.c │ ├── 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 ├── vcf.5 ├── vcf.c ├── vcf_sweep.c └── vcfutils.c ├── install-sh ├── kprobaln.c ├── kprobaln.h ├── misc ├── HmmGlocal.java ├── ace2sam.c ├── blast2sam.pl ├── bowtie2sam.pl ├── export2sam.pl ├── interpolate_sam.pl ├── maq2sam.c ├── md5fa.c ├── md5sum-lite.c ├── novo2sam.pl ├── plot-bamstats ├── psl2sam.pl ├── r2plot.lua ├── sam2vcf.pl ├── samtools.pl ├── seq_cache_populate.pl ├── soap2sam.pl ├── varfilter.py ├── vcfutils.lua ├── wgsim.1 ├── wgsim.c ├── wgsim_eval.pl └── zoom2sam.pl ├── padding.c ├── phase.c ├── sam.c ├── sam.h ├── sam_header.c ├── sam_header.h ├── sam_opts.c ├── sam_opts.h ├── sam_view.c ├── sample.c ├── sample.h ├── samtools.1 ├── samtools.h ├── stats.c ├── stats_isize.c ├── stats_isize.h ├── test ├── addrprg │ ├── 1_fixup.sam │ ├── 1_fixup.sam.expected │ ├── 1_fixup.sam.expected.err │ ├── 2_fixup_orphan.sam │ ├── 2_fixup_orphan.sam.expected │ ├── 2_fixup_orphan.sam.expected.err │ ├── 3_fixup.sam.expected │ ├── 3_fixup.sam.expected.err │ ├── 4_fixup_norg.sam │ ├── 4_fixup_norg.sam.expected │ └── 4_fixup_norg.sam.expected.err ├── bam2fq │ ├── 1.1.fq.expected │ ├── 1.2.fq.expected │ ├── 1.stdout.expected │ ├── 2.1.fq.expected │ ├── 2.2.fq.expected │ ├── 2.s.fq.expected │ ├── 2.stdout.expected │ ├── 3.1.fq.expected │ ├── 3.2.fq.expected │ ├── 3.s.fq.expected │ ├── 3.stdout.expected │ ├── 4.1.fq.expected │ ├── 4.2.fq.expected │ ├── 4.s.fq.expected │ └── 4.stdout.expected ├── dat │ ├── bam2fq.001.sam │ ├── bam2fq.002.sam │ ├── bam2fq.003.sam │ ├── cat.hdr │ ├── cram_md5 │ │ ├── 08c04d512d4797d9ba2a156c1daba468 │ │ ├── 7c35feac7036c1cdef3bee0cc4b21437 │ │ ├── 89b96de7acc5918c2858ef92710be7d4 │ │ └── 8a3d8deb9edd4ce3346b6061fcee6d0b │ ├── depad.001.fa │ ├── depad.001.fa.fai │ ├── depad.001p.sam │ ├── depad.001u.sam │ ├── dict.fa │ ├── dict.out │ ├── empty.expected │ ├── large_chrom.out │ ├── large_chrom.sam │ ├── large_chrom_bai_index.err │ ├── mpileup.1.sam │ ├── mpileup.2.sam │ ├── mpileup.3.sam │ ├── mpileup.err.1 │ ├── mpileup.out.1 │ ├── mpileup.out.2 │ ├── mpileup.out.3 │ ├── mpileup.out.4 │ ├── mpileup.ref.fa │ ├── mpileup.ref.fa.fai │ ├── test_input_1_a.bam │ ├── test_input_1_a.bam.bai.expected │ ├── test_input_1_a.sam │ ├── test_input_1_a_regex.sam │ ├── test_input_1_b.bam │ ├── test_input_1_b.sam │ ├── test_input_1_b_regex.sam │ ├── test_input_1_c.bam │ ├── test_input_1_c.sam │ ├── view.001.01.bed │ ├── view.001.02.bed │ ├── view.001.fa │ ├── view.001.fa.fai │ ├── view.001.sam │ ├── view.002.01.bed │ ├── view.002.02.bed │ ├── view.002.fa │ ├── view.002.fa.fai │ ├── view.002.sam │ ├── view.003.expected.sam │ └── view.003.sam ├── fixmate │ ├── 1_coord_sort.sam │ ├── 1_coord_sort.sam.expected │ ├── 1_coord_sort.sam.expected.err │ ├── 2_isize_overflow.sam │ ├── 2_isize_overflow.sam.expected │ ├── 3_reverse_read_pp_lt.sam │ ├── 3_reverse_read_pp_lt.sam.expected │ ├── 4_reverse_read_pp_equal.sam │ ├── 4_reverse_read_pp_equal.sam.expected │ ├── 5_ct.sam │ ├── 5_ct.sam.expected │ ├── 6_ct_replace.sam │ └── 6_ct_replace.sam.expected ├── idxstats │ ├── test_input_1_a.bam.expected │ └── test_input_1_a.bam.expected.err ├── merge │ ├── 2.merge.expected.bam │ ├── 3.merge.expected.bam │ ├── 3.merge.expected.err │ ├── 4.merge.expected.bam │ ├── 5.merge.expected.bam │ ├── 5.merge.expected.sam │ ├── 6.merge.expected.bam │ ├── 7.merge.expected.bam │ ├── test_3.fofn │ ├── test_bam_translate.c │ ├── test_header.sam │ ├── test_rtrans_build.c │ └── test_trans_tbl_init.c ├── mpileup │ ├── 1read.bam │ ├── 1read.sam │ ├── anomalous.sam │ ├── c1#ID.bam │ ├── c1#ID2.bam │ ├── c1#clip.bam │ ├── c1#pad1.bam │ ├── c1#pad2.bam │ ├── c1#pad3.bam │ ├── c1.fa │ ├── c1.fa.fai │ ├── ce#5b.bam │ ├── ce#5b.bam.bai │ ├── ce#5b.cram │ ├── ce#5b.cram.crai │ ├── ce#5b.sam │ ├── ce#large_seq.bam │ ├── ce#unmap.bam │ ├── ce#unmap1.bam │ ├── ce#unmap2.bam │ ├── ce.fa │ ├── ce.fa.fai │ ├── deep.sam │ ├── depth.reg │ ├── expected │ │ ├── 10.out │ │ ├── 11.out │ │ ├── 12.out │ │ ├── 13.out │ │ ├── 14.out │ │ ├── 15.out │ │ ├── 16.out │ │ ├── 17.out │ │ ├── 18.out │ │ ├── 19.out │ │ ├── 2.out │ │ ├── 20.out │ │ ├── 21.out │ │ ├── 22.out │ │ ├── 23.out │ │ ├── 24.out │ │ ├── 25.out │ │ ├── 26.out │ │ ├── 27.out │ │ ├── 28.out │ │ ├── 29.out │ │ ├── 3.out │ │ ├── 30.out │ │ ├── 31.out │ │ ├── 32.out │ │ ├── 33.out │ │ ├── 34.out │ │ ├── 35.out │ │ ├── 37.out │ │ ├── 38.out │ │ ├── 39.out │ │ ├── 4.out │ │ ├── 40.out │ │ ├── 41.out │ │ ├── 42.out │ │ ├── 43.out │ │ ├── 44.out │ │ ├── 45.out │ │ ├── 46.out │ │ ├── 47.out │ │ ├── 48.out │ │ ├── 49.out │ │ ├── 5.out │ │ ├── 50.out │ │ ├── 51.out │ │ ├── 52.out │ │ ├── 53.out │ │ ├── 54.out │ │ ├── 55.out │ │ ├── 56.out │ │ ├── 57.out │ │ ├── 58.out │ │ ├── 59.out │ │ ├── 6.out │ │ ├── 60.out │ │ ├── 61.out │ │ ├── 62.out │ │ ├── 63.out │ │ ├── 64.out │ │ ├── 65.out │ │ ├── 66.out │ │ ├── 67.out │ │ ├── 68.out │ │ ├── 69.out │ │ ├── 7.out │ │ ├── 70.out │ │ ├── 71.out │ │ ├── 72.out │ │ ├── 73.out │ │ ├── 74.out │ │ ├── 75.out │ │ ├── 76.out │ │ ├── 77.out │ │ ├── 8.out │ │ ├── 9.out │ │ ├── d1_1.out │ │ ├── d1_12.out │ │ ├── d1_2.out │ │ ├── d2_12r.out │ │ ├── d3_12.out │ │ ├── d3_12r1a.out │ │ ├── d3_12r2a.out │ │ ├── d4_12.out │ │ ├── d4_12b.out │ │ └── d4_12r.out │ ├── indels.sam │ ├── md5 │ │ ├── 02099b2aad2cfe707759353724fb40ae │ │ ├── 0d4dfc45807d6a11439e858605cb364d │ │ ├── 351f64d4f4f9ddd45b35336ad97aa6de │ │ ├── 6ec590eb82c361a61e6baabce20109bc │ │ ├── 6f60cdf4c739651ae72d53e2e94825c1 │ │ └── 73d180d5cb3860a2713927b6812eab0e │ ├── mpileup-E.bam │ ├── mpileup.1.bam │ ├── mpileup.1.bam.bai │ ├── mpileup.2.bam │ ├── mpileup.3.bam │ ├── mpileup.ref.fa │ ├── mpileup.ref.fa.fai │ ├── mpileup.reg │ ├── overlap50.sam │ ├── overlapIllumina.bam │ ├── regions │ ├── regression.sh │ ├── xx#depth1.sam │ ├── xx#depth2.sam │ ├── xx#minimal.bam │ ├── xx#triplet.bam │ ├── xx.bed │ ├── xx.bed2 │ ├── xx.fa │ └── xx.fa.fai ├── quickcheck │ ├── 1.quickcheck.badeof.bam │ ├── 2.quickcheck.badheader.bam │ ├── 3.quickcheck.ok.bam │ ├── 4.quickcheck.ok.bam │ ├── 5.quickcheck.truncated.cram │ └── all.expected ├── reheader │ ├── 1_view1.sam.expected │ ├── 1_view1.sam.expected.err │ ├── 2_view1.sam.expected │ ├── 2_view1.sam.expected.err │ ├── 3_view1.sam.expected │ ├── 3_view1.sam.expected.err │ └── hdr.sam ├── split │ ├── test_count_rg.c │ ├── test_expand_format_string.c │ ├── test_filter_header_rg.c │ └── test_parse_args.c ├── stat │ ├── 1.stats.expected │ ├── 10.stats.expected │ ├── 10_map_cigar.sam │ ├── 10_map_cigar.sam_s1_a_1.expected.bamstat │ ├── 10_map_cigar.sam_s1_b_1.expected.bamstat │ ├── 1_map_cigar.sam │ ├── 1_map_cigar.sam_s1_a_1.expected.bamstat │ ├── 2.stats.expected │ ├── 2_equal_cigar_full_seq.sam │ ├── 3.stats.expected │ ├── 3_map_cigar_equal_seq.sam │ ├── 4.stats.expected │ ├── 4_X_cigar_full_seq.sam │ ├── 5.stats.expected │ ├── 5_insert_cigar.sam │ ├── 6.stats.expected │ ├── 7.stats.expected │ ├── 7_supp.sam │ ├── 8.stats.expected │ ├── 8_secondary.sam │ ├── 9.stats.expected │ ├── test.fa │ └── test.fa.fai ├── test.c ├── test.h ├── test.pl ├── tview │ └── test_get_rg_sample.c └── vcf-miniview.c └── win32 ├── libcurses.a ├── libz.a ├── xcurses.h ├── zconf.h └── zlib.h /.gitignore: -------------------------------------------------------------------------------- 1 | # Binaries # 2 | ############ 3 | bin/bgzip 4 | bin/cnvnator-multi 5 | src/cnvnator/bin/cnvnator-multi 6 | bin/cnvnator2VCF.pl 7 | bin/cnvnator_wrapper.py 8 | bin/annotate_rd.py 9 | bin/freebayes 10 | bin/lumpy 11 | bin/lumpyexpress 12 | bin/pairend_distro.py 13 | bin/samblaster 14 | bin/svtyper 15 | bin/tabix 16 | bin/vawk 17 | bin/vcfToBedpe 18 | bin/Bio 19 | bin/bwa 20 | bin/parallel 21 | bin/sambamba 22 | bin/variant_effect_predictor.pl 23 | bin/annotateBed 24 | bin/bamToBed 25 | bin/bamToFastq 26 | bin/bed12ToBed6 27 | bin/bedToBam 28 | bin/bedToIgv 29 | bin/bedpeToBam 30 | bin/bedtools 31 | bin/closestBed 32 | bin/clusterBed 33 | bin/complementBed 34 | bin/coverageBed 35 | bin/expandCols 36 | bin/fastaFromBed 37 | bin/flankBed 38 | bin/genomeCoverageBed 39 | bin/getOverlap 40 | bin/groupBy 41 | bin/intersectBed 42 | bin/linksBed 43 | bin/mapBed 44 | bin/maskFastaFromBed 45 | bin/mergeBed 46 | bin/multiBamCov 47 | bin/multiIntersectBed 48 | bin/nucBed 49 | bin/pairToBed 50 | bin/pairToPair 51 | bin/randomBed 52 | bin/shuffleBed 53 | bin/slopBed 54 | bin/sortBed 55 | bin/subtractBed 56 | bin/tagBam 57 | bin/unionBedGraphs 58 | bin/windowBed 59 | bin/windowMaker 60 | bin/mbuffer 61 | bin/parallel 62 | bin/bamheadrg.py 63 | bin/bamtofastq.py 64 | bin/bamgroupreads.py 65 | bin/bamfilterrg.py 66 | bin/bamcleanheader.py 67 | bin/bamlibs.py 68 | 69 | # Compiled source # 70 | ################### 71 | *.com 72 | *.class 73 | *.dll 74 | *.exe 75 | *.o 76 | *.so 77 | 78 | # Packages # 79 | ############ 80 | # it's better to unpack these files and commit the raw source 81 | # git has its own built in compression methods 82 | *.7z 83 | *.dmg 84 | *.gz 85 | *.iso 86 | *.jar 87 | *.rar 88 | *.tar 89 | *.zip 90 | 91 | # Logs and databases # 92 | ###################### 93 | *.log 94 | *.sql 95 | *.sqlite 96 | 97 | # OS generated files # 98 | ###################### 99 | *~ 100 | \#*\# 101 | .DS_Store 102 | .DS_Store? 103 | ._* 104 | .Spotlight-V100 105 | .Trashes 106 | Icon? 107 | ehthumbs.db 108 | Thumbs.db 109 | 110 | # mbuffer compile files # 111 | ######################### 112 | src/mbuffer/Makefile 113 | src/mbuffer/config.h 114 | src/mbuffer/config.status 115 | src/mbuffer/mbuffer 116 | src/mbuffer/mbuffer.1 -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | [submodule "src/svtyper"] 2 | path = src/svtyper 3 | url = https://github.com/hall-lab/svtyper.git 4 | [submodule "src/samblaster"] 5 | path = src/samblaster 6 | url = https://github.com/GregoryFaust/samblaster.git 7 | [submodule "src/vawk"] 8 | path = src/vawk 9 | url = https://github.com/cc2qe/vawk.git 10 | [submodule "src/tabix"] 11 | path = src/tabix 12 | url = https://github.com/samtools/tabix.git 13 | [submodule "src/freebayes"] 14 | path = src/freebayes 15 | url = https://github.com/ekg/freebayes.git 16 | [submodule "src/bwa"] 17 | path = src/bwa 18 | url = https://github.com/lh3/bwa.git 19 | [submodule "src/bamkit"] 20 | path = src/bamkit 21 | url = https://github.com/cc2qe/bamkit.git 22 | [submodule "src/parallel"] 23 | path = src/parallel 24 | url = http://git.savannah.gnu.org/r/parallel.git 25 | [submodule "src/lumpy-sv"] 26 | path = src/lumpy-sv 27 | url = https://github.com/hall-lab/lumpy-sv.git 28 | branch = 0.2.13_cram_support 29 | [submodule "src/CNVnator"] 30 | path = src/CNVnator 31 | url = https://github.com/abyzovlab/CNVnator 32 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2014 Ira Hall lab 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 all 13 | 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 THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /bin/speedseq.config: -------------------------------------------------------------------------------- 1 | #!/bin/bash -e 2 | 3 | # general 4 | SPEEDSEQ_HOME=/gscmnt/gc2719/halllab/src/speedseq 5 | SAMBAMBA=$SPEEDSEQ_HOME/bin/sambamba 6 | BGZIP=$SPEEDSEQ_HOME/bin/bgzip 7 | TABIX=$SPEEDSEQ_HOME/bin/tabix 8 | VAWK=$SPEEDSEQ_HOME/bin/vawk 9 | PARALLEL=$SPEEDSEQ_HOME/bin/parallel 10 | PYTHON=`which python2.7 || true` # python 2.7 must have numpy, scipy, and pysam installed 11 | 12 | # align 13 | BWA=$SPEEDSEQ_HOME/bin/bwa 14 | SAMBLASTER=$SPEEDSEQ_HOME/bin/samblaster 15 | 16 | # var/somatic 17 | FREEBAYES=$SPEEDSEQ_HOME/bin/freebayes 18 | VEP=$SPEEDSEQ_HOME/bin/variant_effect_predictor.pl 19 | VEP_CACHE_DIR=$SPEEDSEQ_HOME/annotations/vep_cache 20 | 21 | # sv 22 | LUMPYEXPRESS=$SPEEDSEQ_HOME/bin/lumpyexpress 23 | LUMPY=$SPEEDSEQ_HOME/bin/lumpy 24 | PAIREND_DISTRO=$SPEEDSEQ_HOME/bin/pairend_distro.py 25 | SVTYPER=$SPEEDSEQ_HOME/bin/svtyper 26 | BAMGROUPREADS=$SPEEDSEQ_HOME/bin/bamgroupreads.py 27 | BAMFILTERRG=$SPEEDSEQ_HOME/bin/bamfilterrg.py 28 | BAMLIBS=$SPEEDSEQ_HOME/bin/bamlibs.py 29 | 30 | # CNVnator 31 | source /gsc/pkg/root/root/bin/thisroot.sh 32 | CNVNATOR_WRAPPER=$SPEEDSEQ_HOME/bin/cnvnator_wrapper.py 33 | CNVNATOR=$SPEEDSEQ_HOME/bin/cnvnator 34 | ANNOTATE_RD=$SPEEDSEQ_HOME/bin/annotate_rd.py 35 | CNVNATOR_CHROMS_DIR=$SPEEDSEQ_HOME/annotations/cnvnator_chroms 36 | 37 | # re-align 38 | BAMTOFASTQ=$SPEEDSEQ_HOME/bin/bamtofastq.py 39 | MBUFFER=$SPEEDSEQ_HOME/bin/mbuffer 40 | BAMHEADRG=$SPEEDSEQ_HOME/bin/bamheadrg.py 41 | BAMCLEANHEADER=$SPEEDSEQ_HOME/bin/bamcleanheader.py 42 | -------------------------------------------------------------------------------- /etc/add_storage-01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/etc/add_storage-01.png -------------------------------------------------------------------------------- /etc/community_ami-01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/etc/community_ami-01.png -------------------------------------------------------------------------------- /etc/instance_type-01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/etc/instance_type-01.png 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Align with BWA 4 | ../bin/speedseq align \ 5 | -o example \ 6 | -M 3 \ 7 | -p \ 8 | -R "@RG\tID:NA12878\tSM:NA12878\tLB:lib1" \ 9 | data/human_g1k_v37_20_42220611-42542245.fasta \ 10 | data/NA12878.20slice.30X.fastq.gz 11 | 12 | # 2. Detect SNVs and indels 13 | ../bin/speedseq var \ 14 | -o example \ 15 | data/human_g1k_v37_20_42220611-42542245.fasta \ 16 | example.bam 17 | 18 | # 3. Detect SVs 19 | ../bin/speedseq sv \ 20 | -o example \ 21 | -B example.bam \ 22 | -S example.splitters.bam \ 23 | -D example.discordants.bam \ 24 | -R data/human_g1k_v37_20_42220611-42542245.fasta 25 | 26 | # 4. realign with BWA 27 | ../bin/speedseq realign \ 28 | -o example.realign \ 29 | -M 3 \ 30 | data/human_g1k_v37_20_42220611-42542245.fasta \ 31 | example.bam 32 | -------------------------------------------------------------------------------- /src/mbuffer/.hg_archival.txt: -------------------------------------------------------------------------------- 1 | repo: 6e3b485d74645931e2408ed1f57e659029b5639a 2 | node: d98ef1ef3a25043dbae9b29d0f6bd96d873c3934 3 | branch: default 4 | latesttag: R20140310 5 | latesttagdistance: 1 6 | -------------------------------------------------------------------------------- /src/mbuffer/AUTHORS: -------------------------------------------------------------------------------- 1 | Thomas Maier-Komor 2 | e-mail: thomas@maier-komor.de 3 | -------------------------------------------------------------------------------- /src/mbuffer/INSTALL: -------------------------------------------------------------------------------- 1 | # To install run 2 | ./configure 3 | 4 | # with the options you desire. 5 | # To get a list of the possible options, run: 6 | ./configure --help 7 | 8 | # possible options are 9 | ./configure --enable-debug --enable-networking --disable-multivolume 10 | 11 | # Then just do a: 12 | make && make install 13 | -------------------------------------------------------------------------------- /src/mbuffer/NEWS: -------------------------------------------------------------------------------- 1 | See ChangeLog for latest changes... 2 | -------------------------------------------------------------------------------- /src/mbuffer/dest.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2010, Thomas Maier-Komor 3 | * 4 | * This is the source code of mbuffer. 5 | * 6 | * This program is free software: you can redistribute it and/or modify 7 | * it under the terms of the GNU General Public License as published by 8 | * the Free Software Foundation, either version 3 of the License, or 9 | * (at your option) any later version. 10 | * 11 | * This program is distributed in the hope that it will be useful, 12 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | * GNU General Public License for more details. 15 | * 16 | * You should have received a copy of the GNU General Public License 17 | * along with this program. If not, see . 18 | */ 19 | 20 | #ifndef DEST_H 21 | #define DEST_H 22 | 23 | #include 24 | 25 | typedef struct destination { 26 | struct destination *next; 27 | const char *arg, *name, *port, *result; 28 | int fd; 29 | int mode; 30 | pthread_t thread; 31 | } dest_t; 32 | 33 | #endif 34 | -------------------------------------------------------------------------------- /src/mbuffer/log.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2000-2009, Thomas Maier-Komor 3 | * 4 | * This is the source code of mbuffer. 5 | * 6 | * This program is free software: you can redistribute it and/or modify 7 | * it under the terms of the GNU General Public License as published by 8 | * the Free Software Foundation, either version 3 of the License, or 9 | * (at your option) any later version. 10 | * 11 | * This program is distributed in the hope that it will be useful, 12 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | * GNU General Public License for more details. 15 | * 16 | * You should have received a copy of the GNU General Public License 17 | * along with this program. If not, see . 18 | */ 19 | 20 | #ifndef LOG_H 21 | #define LOG_H 22 | 23 | #include "config.h" 24 | 25 | #if !(defined(__sun) || defined(__linux)) 26 | #define NEED_IO_INTERLOCK 27 | #endif 28 | 29 | #ifdef NEED_IO_INTERLOCK 30 | #include 31 | extern pthread_mutex_t LogMut; 32 | #endif 33 | 34 | extern int Verbose, Log, ErrorOccurred, ErrorsFatal; 35 | 36 | #ifdef DEBUG 37 | void logdebug(const char *msg, ...); 38 | #define debugmsg if (Verbose >= 5) logdebug 39 | #define debugiomsg if (Verbose >= 6) logdebug 40 | #elif __STDC_VERSION__ >= 199901L 41 | #define debugmsg(...) 42 | #define debugiomsg(...) 43 | #else 44 | #define debugmsg 45 | #define debugiomsg 46 | #endif 47 | 48 | void infomsg(const char *msg, ...); 49 | void warningmsg(const char *msg, ...); 50 | void errormsg(const char *msg, ...); 51 | void fatal(const char *msg, ...); 52 | 53 | 54 | #endif 55 | -------------------------------------------------------------------------------- /src/mbuffer/network.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2000-2009, Thomas Maier-Komor 3 | * 4 | * This is the source code of mbuffer. 5 | * 6 | * This program is free software: you can redistribute it and/or modify 7 | * it under the terms of the GNU General Public License as published by 8 | * the Free Software Foundation, either version 3 of the License, or 9 | * (at your option) any later version. 10 | * 11 | * This program is distributed in the hope that it will be useful, 12 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | * GNU General Public License for more details. 15 | * 16 | * You should have received a copy of the GNU General Public License 17 | * along with this program. If not, see . 18 | */ 19 | 20 | #ifndef NETWORK_H 21 | #define NETWORK_H 22 | 23 | #include 24 | 25 | extern int32_t TCPBufSize; 26 | extern int AddrFam; 27 | 28 | void initNetworkInput(const char *addr); 29 | struct destination *createNetworkOutput(const char *addr); 30 | 31 | #endif 32 | -------------------------------------------------------------------------------- /src/sambamba: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/sambamba -------------------------------------------------------------------------------- /src/samtools-1.3.1/AUTHORS: -------------------------------------------------------------------------------- 1 | Heng Li from the Sanger Institute wrote most of the initial source codes 2 | of SAMtools and various converters. 3 | 4 | Bob Handsaker from the Broad Institute is a major contributor to the 5 | SAM/BAM specification. He designed and implemented the BGZF format, the 6 | underlying indexable compression format for the BAM format. BGZF does 7 | not support arithmetic between file offsets. 8 | 9 | Jue Ruan for the Beijing Genome Institute designed and implemented the 10 | RAZF format, an alternative indexable compression format. RAZF is no longer 11 | used by or provided with SAMtools. Source code remains available in older 12 | SAMtools 0.1.x releases and from the standalone branch in the repository. 13 | 14 | Colin Hercus updated novo2sam.pl to support gapped alignment by 15 | novoalign. 16 | 17 | Petr Danecek contributed the header parsing library sam_header.c and 18 | sam2vcf.pl script. 19 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/LICENSE: -------------------------------------------------------------------------------- 1 | The MIT/Expat License 2 | 3 | Copyright (C) 2008-2014 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 | 24 | [The use of a range of years within a copyright notice in this distribution 25 | should be interpreted as being equivalent to a list of years including the 26 | first and last year specified and all consecutive years between them. 27 | 28 | For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009, 29 | 2011-2012" should be interpreted as being identical to a notice that reads 30 | "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice 31 | that reads "Copyright (C) 2005-2012" should be interpreted as being identical 32 | to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 33 | 2011, 2012".] 34 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/Makefile.mingw: -------------------------------------------------------------------------------- 1 | CC= gcc.exe 2 | AR= ar.exe 3 | CFLAGS= -g -Wall -O2 4 | DFLAGS= -D_USE_KNETFILE -D_CURSES_LIB=2 5 | KNETFILE_O= knetfile.o 6 | LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ 7 | bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \ 8 | $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o 9 | AOBJS= bam_tview.o bam_plcmd.o sam_view.o \ 10 | bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ 11 | bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \ 12 | cut_target.o phase.o bam_cat.o bam2depth.o 13 | BCFOBJS= bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \ 14 | bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \ 15 | bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o 16 | PROG= samtools.exe bcftools.exe 17 | INCLUDES= -I. -Iwin32 18 | SUBDIRS= . 19 | LIBPATH= 20 | 21 | .SUFFIXES:.c .o 22 | 23 | .c.o: 24 | $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ 25 | 26 | all:$(PROG) 27 | 28 | .PHONY:all lib clean cleanlocal 29 | .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur 30 | 31 | lib:libbam.a 32 | 33 | libbam.a:$(LOBJS) 34 | $(AR) -cru $@ $(LOBJS) 35 | 36 | samtools.exe:$(AOBJS) libbam.a $(BCFOBJS) 37 | $(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32 38 | 39 | bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o 40 | $(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32 41 | 42 | razip.o:razf.h 43 | bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h 44 | sam.o:sam.h bam.h 45 | bam_import.o:bam.h kseq.h khash.h razf.h 46 | bam_pileup.o:bam.h razf.h ksort.h 47 | bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h 48 | bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h 49 | bam_lpileup.o:bam.h ksort.h 50 | bam_tview.o:bam.h faidx.h 51 | bam_sort.o:bam.h ksort.h razf.h 52 | bam_md.o:bam.h faidx.h 53 | sam_header.o:sam_header.h khash.h 54 | bcf.o:bcftools/bcf.h 55 | bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h 56 | bam2bcf_indel.o:bam2bcf.h 57 | errmod.o:errmod.h 58 | 59 | faidx.o:faidx.h razf.h khash.h 60 | faidx_main.o:faidx.h razf.h 61 | 62 | clean: 63 | rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib 64 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/README: -------------------------------------------------------------------------------- 1 | Samtools implements various utilities for post-processing alignments in the 2 | SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction 3 | with bcftools), and a simple alignment viewer. 4 | 5 | 6 | Building samtools 7 | ================= 8 | 9 | The typical simple case of building Samtools using the HTSlib bundled within 10 | this Samtools release tarball and enabling useful plugins, is done as follows: 11 | 12 | cd .../samtools-1.3.1 # Within the unpacked release directory 13 | ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 14 | make all plugins-htslib 15 | 16 | You may wish to copy the resulting samtools executable into somewhere on your 17 | $PATH, or run it where it is. 18 | 19 | Rather than running-in-place like that, the next simplest typical case is to 20 | install samtools etc properly into a directory of your choosing. Building for 21 | installation using the HTSlib bundled within this Samtools release tarball, 22 | also building the various HTSlib utilities such as bgzip and enabling useful 23 | plugins, is done as follows: 24 | 25 | cd .../samtools-1.3.1 # Within the unpacked release directory 26 | ./configure --enable-plugins --enable-libcurl --prefix=/path/to/location 27 | make all all-htslib 28 | make install install-htslib 29 | 30 | You will likely wish to add /path/to/location/bin to your $PATH. 31 | 32 | See INSTALL for full building and installation instructions and details. 33 | 34 | 35 | Using an optimised zlib library 36 | =============================== 37 | 38 | Samtools has been minimally tested against both the Intel-optimised and 39 | CloudFlare-optimised zlibs and shown to work. 40 | 41 | They can be downloaded from: 42 | 43 | https://github.com/jtkukunas/zlib # Intel 44 | https://github.com/cloudflare/zlib # CloudFlare 45 | 46 | Neither Samtools nor HTSlib needs recompiling to use these optimised libraries, 47 | but the LD_LIBRARY_PATH environment variable should be set to a directory 48 | containing the libz.so.1 file. 49 | 50 | Benchmarks comparing the various zlibs are available at: 51 | 52 | http://www.htslib.org/benchmarks/zlib.html 53 | 54 | It is recommended that you perform your own rigorous tests for an entire 55 | pipeline if you wish to switch to one of the optimised zlib implementations. 56 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/bam_lpileup.h: -------------------------------------------------------------------------------- 1 | /* bam_lpileup.h -- lplbuf routines (declarations copied from bam.h). 2 | 3 | Copyright (C) 2008, 2013 Genome Research Ltd. 4 | 5 | Author: Heng Li 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 BAM_LPILEUP_H 26 | #define BAM_LPILEUP_H 27 | 28 | 29 | #include 30 | 31 | struct __bam_lplbuf_t; 32 | typedef struct __bam_lplbuf_t bam_lplbuf_t; 33 | 34 | #ifndef BAM_PILEUP_F_DEFINED 35 | #define BAM_PILEUP_F_DEFINED 36 | typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); 37 | #endif //BAM_PILEUP_F_DEFINED 38 | 39 | 40 | #ifdef __cplusplus 41 | extern "C" { 42 | #endif 43 | void bam_lplbuf_reset(bam_lplbuf_t *buf); 44 | 45 | /*! @abstract bam_plbuf_init() equivalent with level calculated. */ 46 | bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data); 47 | 48 | /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */ 49 | void bam_lplbuf_destroy(bam_lplbuf_t *tv); 50 | 51 | /*! @abstract bam_plbuf_push() equivalent with level calculated. */ 52 | int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf); 53 | #ifdef __cplusplus 54 | } 55 | #endif 56 | 57 | #endif // BAM_LPILEUP_H 58 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/bam_plbuf.h: -------------------------------------------------------------------------------- 1 | /* bam_plbuf.h -- plbuf routines (declarations copied from bam.h). 2 | 3 | Copyright (C) 2008, 2013 Genome Research Ltd. 4 | 5 | Author: Heng Li 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 BAM_PLBUF_H 26 | #define BAM_PLBUF_H 27 | 28 | #include 29 | 30 | #ifndef BAM_PILEUP_F_DEFINED 31 | #define BAM_PILEUP_F_DEFINED 32 | typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); 33 | #endif //BAM_PILEUP_F_DEFINED 34 | 35 | typedef struct { 36 | bam_plp_t iter; 37 | bam_pileup_f func; 38 | void *data; 39 | } bam_plbuf_t; 40 | 41 | #ifdef __cplusplus 42 | extern "C" { 43 | #endif 44 | void bam_plbuf_reset(bam_plbuf_t *buf); 45 | 46 | bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data); 47 | 48 | void bam_plbuf_destroy(bam_plbuf_t *buf); 49 | 50 | int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf); 51 | #ifdef __cplusplus 52 | } 53 | #endif 54 | 55 | #endif // BAM_PLBUF_H 56 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/config.h.in: -------------------------------------------------------------------------------- 1 | /* config.h.in -- template for config.h. If you use configure, this file 2 | provides #defines reflecting your configuration choices. If you don't 3 | run configure, suitable conservative defaults will be used. 4 | 5 | This template file can be updated with autoheader, but do so carefully 6 | as autoheader adds #defines such as PACKAGE_* that we don't want. */ 7 | 8 | /* Define to 1 if a SysV or X/Open compatible Curses library is present */ 9 | #undef HAVE_CURSES 10 | 11 | /* Define to 1 if library supports color (enhanced functions) */ 12 | #undef HAVE_CURSES_COLOR 13 | 14 | /* Define to 1 if library supports X/Open Enhanced functions */ 15 | #undef HAVE_CURSES_ENHANCED 16 | 17 | /* Define to 1 if is present */ 18 | #undef HAVE_CURSES_H 19 | 20 | /* Define to 1 if library supports certain obsolete features */ 21 | #undef HAVE_CURSES_OBSOLETE 22 | 23 | /* Define to 1 if the Ncurses library is present */ 24 | #undef HAVE_NCURSES 25 | 26 | /* Define to 1 if the NcursesW library is present */ 27 | #undef HAVE_NCURSESW 28 | 29 | /* Define to 1 if is present */ 30 | #undef HAVE_NCURSESW_CURSES_H 31 | 32 | /* Define to 1 if is present */ 33 | #undef HAVE_NCURSESW_H 34 | 35 | /* Define to 1 if is present */ 36 | #undef HAVE_NCURSES_CURSES_H 37 | 38 | /* Define to 1 if is present */ 39 | #undef HAVE_NCURSES_H 40 | 41 | /* Enable large inode numbers on Mac OS X 10.5. */ 42 | #ifndef _DARWIN_USE_64_BIT_INODE 43 | # define _DARWIN_USE_64_BIT_INODE 1 44 | #endif 45 | 46 | /* Number of bits in a file offset, on hosts where this is settable. */ 47 | #undef _FILE_OFFSET_BITS 48 | 49 | /* Define for large files, on AIX-style hosts. */ 50 | #undef _LARGE_FILES 51 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/config.mk.in: -------------------------------------------------------------------------------- 1 | # Optional configure Makefile overrides for samtools. 2 | # 3 | # Copyright (C) 2015 Genome Research Ltd. 4 | # 5 | # Author: John Marshall 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 | # This is @configure_input@ 26 | # 27 | # If you use configure, this file overrides variables and augments rules 28 | # in the Makefile to reflect your configuration choices. If you don't run 29 | # configure, the main Makefile contains suitable conservative defaults. 30 | 31 | prefix = @prefix@ 32 | exec_prefix = @exec_prefix@ 33 | bindir = @bindir@ 34 | datarootdir = @datarootdir@ 35 | mandir = @mandir@ 36 | 37 | CC = @CC@ 38 | CPPFLAGS = @CPPFLAGS@ 39 | CFLAGS = @CFLAGS@ 40 | LDFLAGS = @LDFLAGS@ 41 | LIBS = @LIBS@ 42 | 43 | @Hsource@HTSDIR = @HTSDIR@ 44 | @Hsource@include $(HTSDIR)/htslib.mk 45 | @Hsource@HTSLIB = $(HTSDIR)/libhts.a 46 | @Hsource@HTSLIB_LIB = $(HTSLIB) 47 | @Hsource@BGZIP = $(HTSDIR)/bgzip 48 | HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@ 49 | @Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@ 50 | @Hinstall@HTSLIB_LIB = -lhts 51 | 52 | CURSES_LIB = @CURSES_LIB@ 53 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/errmod.h: -------------------------------------------------------------------------------- 1 | /* errmod.h -- revised MAQ error model. 2 | 3 | Copyright (C) 2010 Broad Institute. 4 | Copyright (C) 2012 Genome Research Ltd. 5 | 6 | Author: Heng Li 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 ERRMOD_H 27 | #define ERRMOD_H 28 | 29 | #include 30 | 31 | struct __errmod_coef_t; 32 | 33 | typedef struct { 34 | double depcorr; 35 | struct __errmod_coef_t *coef; 36 | } errmod_t; 37 | 38 | errmod_t *errmod_init(double depcorr); 39 | void errmod_destroy(errmod_t *em); 40 | 41 | /* 42 | n: number of bases 43 | m: maximum base 44 | bases[i]: qual:6, strand:1, base:4 45 | q[i*m+j]: phred-scaled likelihood of (i,j) 46 | */ 47 | int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); 48 | 49 | #endif 50 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/examples/00README.txt: -------------------------------------------------------------------------------- 1 | File ex1.fa contains two sequences cut from the human genome 2 | build36. They were extracted with command: 3 | 4 | samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550 5 | 6 | Sequence names were changed manually for simplicity. File ex1.sam.gz 7 | contains MAQ alignments extracted with: 8 | 9 | (samtools view NA18507_maq.bam 2:2044001-2045500; 10 | samtools view NA18507_maq.bam 20:68001-69500) 11 | 12 | and processed with `samtools fixmate' to make it self-consistent as a 13 | standalone alignment. 14 | 15 | To try samtools, you may run the following commands. 16 | 17 | Index the reference FASTA. 18 | samtools faidx ex1.fa 19 | 20 | Convert the (headerless) SAM file to BAM. Note if we had used 21 | "samtools view -h" above to create the ex1.sam.gz then we could omit the 22 | "-t ex1.fa.fai" option here. 23 | samtools view -S -b -t ex1.fa.fai -o ex1.bam ex1.sam.gz 24 | 25 | Build an index for the BAM file: 26 | samtools index ex1.bam 27 | 28 | View a portion of the BAM file: 29 | samtools view ex1.bam seq2:450-550 30 | 31 | Visually inspect the alignments at the same location: 32 | samtools tview -p seq2:450 ex1.bam ex1.fa 33 | 34 | View the data in pileup format: 35 | samtools mpileup -f ex1.fa ex1.bam 36 | 37 | Generate an uncompressed VCF file of variants: 38 | samtools mpileup -vu -f ex1.fa ex1.bam > ex1.vcf 39 | 40 | Generate a compressed VCF file of variants: 41 | samtools mpileup -g -f ex1.fa ex1.bam > ex1.bcf 42 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/examples/toy.fa: -------------------------------------------------------------------------------- 1 | >ref 2 | AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT 3 | >ref2 4 | aggttttataaaacaattaagtctacagagcaactacgcg 5 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/examples/toy.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref LN:45 2 | @SQ SN:ref2 LN:40 3 | r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 4 | r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * 5 | r003 0 ref 9 30 5H6M * 0 0 AGCTAA * 6 | r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 7 | r003 16 ref 29 30 6H5M * 0 0 TAGGC * 8 | r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * 9 | x1 0 ref2 1 30 20M * 0 0 aggttttataaaacaaataa ???????????????????? 10 | x2 0 ref2 2 30 21M * 0 0 ggttttataaaacaaataatt ????????????????????? 11 | x3 0 ref2 6 30 9M4I13M * 0 0 ttataaaacAAATaattaagtctaca ?????????????????????????? 12 | x4 0 ref2 10 30 25M * 0 0 CaaaTaattaagtctacagagcaac ????????????????????????? 13 | x5 0 ref2 12 30 24M * 0 0 aaTaattaagtctacagagcaact ???????????????????????? 14 | x6 0 ref2 14 30 23M * 0 0 Taattaagtctacagagcaacta ??????????????????????? 15 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/config.h.in: -------------------------------------------------------------------------------- 1 | /* config.h.in -- template for config.h. If you use configure, this file 2 | provides #defines reflecting your configuration choices. If you don't 3 | run configure, suitable conservative defaults will be used. 4 | 5 | This template file can be updated with autoheader, but do so carefully 6 | as autoheader adds #defines such as PACKAGE_* that we don't want. */ 7 | 8 | /* Define if HTSlib should enable plugins. */ 9 | #undef ENABLE_PLUGINS 10 | 11 | /* Define if you have the Common Crypto library. */ 12 | #undef HAVE_COMMONCRYPTO 13 | 14 | /* Define to 1 if you have the `gmtime_r' function. */ 15 | #undef HAVE_GMTIME_R 16 | 17 | /* Define if you have libcrypto-style HMAC(). */ 18 | #undef HAVE_HMAC 19 | 20 | /* Define to 1 if iRODS file access is enabled. */ 21 | #undef HAVE_IRODS 22 | 23 | /* Define if libcurl file access is enabled. */ 24 | #undef HAVE_LIBCURL 25 | 26 | /* Define to 1 if you have a working `mmap' system call. */ 27 | #undef HAVE_MMAP 28 | 29 | /* Enable large inode numbers on Mac OS X 10.5. */ 30 | #ifndef _DARWIN_USE_64_BIT_INODE 31 | # define _DARWIN_USE_64_BIT_INODE 1 32 | #endif 33 | 34 | /* Number of bits in a file offset, on hosts where this is settable. */ 35 | #undef _FILE_OFFSET_BITS 36 | 37 | /* Define for large files, on AIX-style hosts. */ 38 | #undef _LARGE_FILES 39 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/cram/vlen.h: -------------------------------------------------------------------------------- 1 | /* 2 | Author: James Bonfield (jkb@sanger.ac.uk) 3 | 4 | Copyright (c) 1995-1996 MEDICAL RESEARCH COUNCIL 5 | All rights reserved 6 | 7 | Redistribution and use in source and binary forms, with or without 8 | modification, are permitted provided that the following conditions are met: 9 | 10 | 1 Redistributions of source code must retain the above copyright notice, 11 | this list of conditions and the following disclaimer. 12 | 13 | 2 Redistributions in binary form must reproduce the above copyright notice, 14 | this list of conditions and the following disclaimer in the documentation 15 | and/or other materials provided with the distribution. 16 | 17 | 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 18 | MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 19 | promote products derived from this software without specific prior written 20 | permission. 21 | 22 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 23 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 24 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 25 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 26 | ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 27 | (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 28 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 29 | ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 30 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 31 | SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 32 | */ 33 | 34 | #ifndef _VLEN_H_ 35 | #define _VLEN_H_ 36 | 37 | #ifdef __cplusplus 38 | extern "C" { 39 | #endif 40 | 41 | extern int vflen(char *fmt, va_list ap); 42 | extern int flen(char *fmt, ...); 43 | 44 | #ifdef __cplusplus 45 | } 46 | #endif 47 | 48 | #endif /* _VLEN_H_ */ 49 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/cram/zfio.h: -------------------------------------------------------------------------------- 1 | /* 2 | Copyright (c) 2009-2013 Genome Research Ltd. 3 | Author: 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 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 _ZFIO_H_ 32 | #define _ZFIO_H_ 33 | 34 | #include 35 | #include 36 | 37 | #ifdef __cplusplus 38 | extern "C" { 39 | #endif 40 | 41 | /* 42 | * Either a gzFile or a FILE. 43 | */ 44 | typedef struct { 45 | FILE *fp; 46 | gzFile gz; 47 | } zfp; 48 | 49 | off_t zftello(zfp *zf); 50 | int zfseeko(zfp *zf, off_t offset, int whence); 51 | char *zfgets(char *line, int size, zfp *zf); 52 | int zfputs(char *line, zfp *zf); 53 | zfp *zfopen(const char *path, const char *mode); 54 | int zfclose(zfp *zf); 55 | int zfpeek(zfp *zf); 56 | int zfeof(zfp *zf); 57 | 58 | #ifdef __cplusplus 59 | } 60 | #endif 61 | 62 | #endif /* _ZFIO_H_ */ 63 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/htslib.pc.in: -------------------------------------------------------------------------------- 1 | includedir=@includedir@ 2 | libdir=@libdir@ 3 | 4 | Name: htslib 5 | Description: C library for high-throughput sequencing data formats 6 | Version: @PACKAGE_VERSION@ 7 | Cflags: -I${includedir} 8 | Libs: -L${libdir} -lhts 9 | Libs.private: -L${libdir} -lhts -lm -lpthread 10 | Requires.private: zlib 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/htslib/vcf_sweep.h: -------------------------------------------------------------------------------- 1 | /* vcf_sweep.h -- forward/reverse sweep API. 2 | 3 | Copyright (C) 2013 Genome Research Ltd. 4 | 5 | Author: Petr Danecek 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_VCF_SWEEP_H 26 | #define HTSLIB_VCF_SWEEP_H 27 | 28 | #include "hts.h" 29 | #include "vcf.h" 30 | 31 | #ifdef __cplusplus 32 | extern "C" { 33 | #endif 34 | 35 | typedef struct _bcf_sweep_t bcf_sweep_t; 36 | 37 | bcf_sweep_t *bcf_sweep_init(const char *fname); 38 | void bcf_sweep_destroy(bcf_sweep_t *sw); 39 | bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw); 40 | bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw); 41 | bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw); 42 | 43 | #ifdef __cplusplus 44 | } 45 | #endif 46 | 47 | #endif 48 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/aux#aux_java.cram: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/htslib-1.3.1/test/aux#aux_java.cram -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 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 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/auxf.fa: -------------------------------------------------------------------------------- 1 | >Sheila 2 | GCTAGCTCAGAAAAAAAAAA 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/auxf.fa.fai: -------------------------------------------------------------------------------- 1 | Sheila 20 8 20 21 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/c1.fa: -------------------------------------------------------------------------------- 1 | >c1 2 | AACCGCGGTT 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/c1.fa.fai: -------------------------------------------------------------------------------- 1 | c1 10 4 10 11 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/c2.fa: -------------------------------------------------------------------------------- 1 | >c2 2 | CCAATAACC 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/c2.fa.fai: -------------------------------------------------------------------------------- 1 | c2 9 4 9 10 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/ce#5b_java.cram: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/htslib-1.3.1/test/ce#5b_java.cram -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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!"#$%25^&*()_+<>?:@~{}%7C%0A1234567890-=[]'%3B#,./\ 11 | * 768 CHROMOSOME_I 101 255 1M * 0 0 * * CT:Z:+;STOP 12 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/ce#tag_padded.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @RG ID:UNKNOWN SM:unknown LB:UNKNOWN 3 | @SQ SN:CHROMOSOME_I LN:1009800 4 | I 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC PT:Z:27;29;+;STOP;Note=tag1 5 | II.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC PT:Z:27;27;+;PRIM;Note=tag2|29;29;+;OLIG;Note=tag3 6 | III 0 CHROMOSOME_I 2 1 101M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTCAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###########################"##@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC PT:Z:1;1;+;COMM|101;101;+;COMM 7 | IV 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 8 | V 0 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 9 | * 768 CHROMOSOME_I 2 255 1M * 0 0 * * CT:Z:+;STOP 10 | * 768 CHROMOSOME_I 28 255 3M * 0 0 * * CT:Z:+;COMM;Note=consensus%0Amulti%09line%0Atag%0A!"#$%25^&*()_+<>?:@~{}%7C%0A1234567890-=[]'%3B#,./\ 11 | * 768 CHROMOSOME_I 102 255 1M * 0 0 * * CT:Z:+;STOP 12 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | > foo 14 | TGCATG 15 | CA 16 | > bar description 17 | TTTTAAAA 18 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/formatcols.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##FILTER= 3 | ##contig= 4 | ##FORMAT= 5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 6 | 1 100 a A T . . . S a bbbbbbb ccccccccc 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/noroundtrip-out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##FILTER= 3 | ##contig= 4 | ##FORMAT= 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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/noroundtrip.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##contig= 3 | ##FORMAT= 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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/test-vcf-api.out: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##FILTER= 3 | ##fileDate=20090805 4 | ##unused= 5 | ##source=myImputationProgramV3.1 6 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 7 | ##contig= 8 | ##phasing=partial 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##INFO= 15 | ##FILTER= 16 | ##FILTER= 17 | ##FORMAT= 18 | ##FORMAT= 19 | ##FORMAT= 20 | ##FORMAT= 21 | ##FORMAT= 22 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 23 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:TS 0|0:48:1:51,51:String1 1|0:48:8:51,51:SomeOtherString2 1/1:43:5:.,.:YetAnotherString3 24 | 20 14370 . G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:DP:HQ:TS 0|0:1:51,51:String1 1|0:8:51,51:SomeOtherString2 1/1:5:.,.:YetAnotherString3 25 | 20 14370 . G A 29 PASS NS=3;DP=99;AF=0.5;DB;H2 GT:DP:HQ:TS 0|0:9:51,51:String1 1|0:9:51,51:SomeOtherString2 1/1:9:.,.:YetAnotherString3 26 | 20 1110696 . A G,T 67 . NS=2;DP=10;AF=0.333,.;AA=T;DB GT 2 1 ./. 27 | 20 1110696 . A G,T 67 . NS=2;DP=10;AF=0.333,.;AA=T;DB GT 2 1 ./. 28 | 20 1110696 . G A 67 . NS=2;DP=99;AF=0.333,.;AA=T;DB GT:DP 2:9 1:9 ./.:9 29 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/test-vcf-hdr-in.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20150126 3 | ##reference=hs37d5 4 | ##phasing=partial 5 | ##FILTER= 200.0"> 6 | ##FILTER= 7 | ##FILTER= 8 | ##FILTER= 9 | ##INFO= 10 | ##FORMAT= 11 | ##FORMAT= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/test-vcf-hdr.out: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##fileDate=20150126 4 | ##reference=hs37d5 5 | ##phasing=partial 6 | ##FILTER= 200.0"> 7 | ##FILTER= 8 | ##FILTER= 9 | ##FILTER= 10 | ##INFO= 11 | ##FORMAT= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | ##FORMAT= 16 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 17 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/test-vcf-sweep.out: -------------------------------------------------------------------------------- 1 | fwd position chksum: 1125066 2 | bwd position chksum: 1125066 3 | fwd PL chksum: 0 4 | bwd PL chksum: 0 5 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/xx#blank.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/htslib-1.3.1/test/xx#blank.sam -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/xx#large_aux_java.cram: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/htslib-1.3.1/test/xx#large_aux_java.cram -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/xx.fa: -------------------------------------------------------------------------------- 1 | >xx 2 | AAAAAAAAAATTTTTTTTTT 3 | >yy 4 | AAAAAAAAAATTTTTTTTTT 5 | 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/htslib-1.3.1/test/xx.fa.fai: -------------------------------------------------------------------------------- 1 | xx 20 4 20 21 2 | yy 20 29 20 21 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/kprobaln.h: -------------------------------------------------------------------------------- 1 | /* The MIT License 2 | 3 | Copyright (C) 2003-2006, 2008-2010 by Heng Li 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 | #ifndef LH3_KPROBALN_H_ 27 | #define LH3_KPROBALN_H_ 28 | 29 | #include 30 | 31 | typedef struct { 32 | float d, e; 33 | int bw; 34 | } kpa_par_t; 35 | 36 | #ifdef __cplusplus 37 | extern "C" { 38 | #endif 39 | 40 | int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual, 41 | const kpa_par_t *c, int *state, uint8_t *q); 42 | 43 | #ifdef __cplusplus 44 | } 45 | #endif 46 | 47 | extern kpa_par_t kpa_par_def, kpa_par_alt; 48 | 49 | #endif 50 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/misc/md5sum-lite.c: -------------------------------------------------------------------------------- 1 | /* md5sum-lite.c -- Basic md5sum implementation. 2 | 3 | Copyright (C) 2008, 2009 Genome Research Ltd. 4 | 5 | Author: Heng Li 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 26 | 27 | #include 28 | #include 29 | #include 30 | #include "htslib/hts.h" 31 | 32 | static void md5_one(const char *fn) 33 | { 34 | unsigned char buf[4096], digest[16]; 35 | char hex[33]; 36 | hts_md5_context *md5; 37 | int l; 38 | FILE *fp; 39 | 40 | fp = strcmp(fn, "-")? fopen(fn, "r") : stdin; 41 | if (fp == 0) { 42 | fprintf(stderr, "md5sum: %s: No such file or directory\n", fn); 43 | exit(1); 44 | } 45 | if (!(md5 = hts_md5_init())) { 46 | fprintf(stderr, "md5sum: %s: Failed to allocate md5 buffer\n", fn); 47 | exit(1); 48 | } 49 | while ((l = fread(buf, 1, 4096, fp)) > 0) 50 | hts_md5_update(md5, buf, l); 51 | hts_md5_final(digest, md5); 52 | if (fp != stdin) fclose(fp); 53 | hts_md5_hex(hex, digest); 54 | printf("%s %s\n", hex, fn); 55 | hts_md5_destroy(md5); 56 | } 57 | int main(int argc, char *argv[]) 58 | { 59 | int i; 60 | if (argc == 1) md5_one("-"); 61 | else for (i = 1; i < argc; ++i) md5_one(argv[i]); 62 | return 0; 63 | } 64 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/misc/wgsim.1: -------------------------------------------------------------------------------- 1 | .TH wgsim 1 "22 April 2016" "samtools-1.3.1" "Bioinformatics tools" 2 | .SH NAME 3 | wgsim \- Whole-genome sequencing read simulator 4 | .SH SYNOPSIS 5 | .B wgsim 6 | [\fI\,options\/\fR] \fI\, \/\fR 7 | .PP 8 | must be a fasta file containing a reference genome. 9 | .PP 10 | and are the first and second read output files. 11 | .SH OPTIONS 12 | .TP 13 | \fB\-e\fR FLOAT 14 | base error rate [0.000] 15 | .TP 16 | \fB\-d\fR INT 17 | outer distance between the two ends [500] 18 | .TP 19 | \fB\-s\fR INT 20 | standard deviation [50] 21 | .TP 22 | \fB\-N\fR INT 23 | number of read pairs [1000000] 24 | .TP 25 | \fB\-1\fR INT 26 | length of the first read [70] 27 | .TP 28 | \fB\-2\fR INT 29 | length of the second read [70] 30 | .TP 31 | \fB\-r\fR FLOAT 32 | rate of mutations [0.0010] 33 | .TP 34 | \fB\-R\fR FLOAT 35 | fraction of indels [0.15] 36 | .TP 37 | \fB\-X\fR FLOAT 38 | probability an indel is extended [0.30] 39 | .TP 40 | \fB\-S\fR INT 41 | seed for random generator [\-1] 42 | .TP 43 | \fB\-A\fR FLOAT 44 | discard if the fraction of ambiguous bases higher than FLOAT [0.05] 45 | .TP 46 | \fB\-h\fR 47 | haplotype mode 48 | .TP 49 | Parameter defaults are given in square brackets. 50 | .SH AUTHOR 51 | Copyright 2008 Genome Research Limited. 52 | .br 53 | Copyright 2011 Heng Li. 54 | .TP 55 | wgsim is part of samtools, https://github.com/samtools/samtools 56 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/sample.h: -------------------------------------------------------------------------------- 1 | /* sample.h -- group data by sample. 2 | 3 | Copyright (C) 2010 Broad Institute. 4 | 5 | Author: Heng Li 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 BAM_SAMPLE_H 26 | #define BAM_SAMPLE_H 27 | 28 | #include "htslib/kstring.h" 29 | 30 | typedef struct { 31 | int n, m; 32 | char **smpl; 33 | void *rg2smid, *sm2id; 34 | } bam_sample_t; 35 | 36 | bam_sample_t *bam_smpl_init(void); 37 | int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt); 38 | int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str); 39 | void bam_smpl_destroy(bam_sample_t *sm); 40 | 41 | #endif 42 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/samtools.h: -------------------------------------------------------------------------------- 1 | /* samtools.h -- utility routines. 2 | 3 | Copyright (C) 2013-2015 Genome Research Ltd. 4 | 5 | Author: Petr Danecek 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 SAMTOOLS_H 26 | #define SAMTOOLS_H 27 | 28 | const char *samtools_version(void); 29 | 30 | #if defined __GNUC__ && __GNUC__ >= 2 31 | #define CHECK_PRINTF(fmt,args) __attribute__ ((format (printf, fmt, args))) 32 | #else 33 | #define CHECK_PRINTF(fmt,args) 34 | #endif 35 | 36 | void print_error(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3); 37 | void print_error_errno(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3); 38 | 39 | #endif 40 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/1_fixup.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:1#8 CN:SC 5 | @RG ID:1#7 CN:SC 6 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 7 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 9 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 10 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * 11 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * 12 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#7 13 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 14 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * 15 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * 16 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 17 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 18 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 19 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 20 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 21 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 22 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 23 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 24 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 25 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 26 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 27 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 28 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 29 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 30 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 31 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/1_fixup.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:1#8 CN:SC 5 | @RG ID:1#7 CN:SC 6 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:1#8 7 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:1#8 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:1#8 9 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:1#8 10 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:1#8 11 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:1#8 12 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#8 13 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#8 14 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:1#8 15 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:1#8 16 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:1#8 17 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:1#8 18 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:1#8 19 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:1#8 20 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:1#8 21 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:1#8 22 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:1#8 23 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:1#8 24 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:1#8 25 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:1#8 26 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:1#8 27 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:1#8 28 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 29 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 30 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 31 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/1_fixup.sam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/addrprg/1_fixup.sam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/2_fixup_orphan.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:1#8 CN:SC 5 | @RG ID:1#7 CN:SC 6 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 7 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 9 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 10 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * 11 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * 12 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#7 13 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 14 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * 15 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * 16 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 17 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 18 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 19 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 20 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 21 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 22 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 23 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 24 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 25 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 26 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 27 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 28 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 29 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 30 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 31 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/2_fixup_orphan.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:1#8 CN:SC 5 | @RG ID:1#7 CN:SC 6 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:1#8 7 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:1#8 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:1#8 9 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:1#8 10 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:1#8 11 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:1#8 12 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#7 13 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#8 14 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:1#8 15 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:1#8 16 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:1#8 17 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:1#8 18 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:1#8 19 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:1#8 20 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:1#8 21 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:1#8 22 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:1#8 23 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:1#8 24 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:1#8 25 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:1#8 26 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:1#8 27 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:1#8 28 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 29 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 30 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 31 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/2_fixup_orphan.sam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/addrprg/2_fixup_orphan.sam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/3_fixup.sam.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/addrprg/3_fixup.sam.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/3_fixup.sam.expected.err: -------------------------------------------------------------------------------- 1 | RG ID supplied does not exist in header. Supply full @RG line with -r instead? 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/4_fixup_norg.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:1#7 CN:SC 5 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 6 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 7 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 8 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 9 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * 10 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * 11 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#7 12 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 13 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * 14 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * 15 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 16 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 17 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 18 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 19 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 20 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 21 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 22 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 23 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 24 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 25 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 26 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 27 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 28 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 29 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 30 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/4_fixup_norg.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:1#7 CN:SC 5 | @RG ID:1#8 CN:SC 6 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:1#8 7 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:1#8 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:1#8 9 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:1#8 10 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:1#8 11 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:1#8 12 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#8 13 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:1#8 14 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:1#8 15 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:1#8 16 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:1#8 17 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:1#8 18 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:1#8 19 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:1#8 20 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:1#8 21 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:1#8 22 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:1#8 23 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:1#8 24 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:1#8 25 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:1#8 26 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:1#8 27 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:1#8 28 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 29 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 30 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:1#8 31 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/addrprg/4_fixup_norg.sam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/addrprg/4_fixup_norg.sam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/1.1.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | CGAGCTCGGT 3 | + 4 | !!!!!!!!!! 5 | @ref1_grp1_p002 6 | CTCGGTACCC 7 | + 8 | ########## 9 | @ref1_grp1_p003 10 | GTACCCGGGG 11 | + 12 | %%%%%%%%%% 13 | @ref1_grp1_p004 14 | CCGGGGATCC 15 | + 16 | '''''''''' 17 | @ref1_grp1_p005 18 | GGATCCTCTA 19 | + 20 | )))))))))) 21 | @ref1_grp1_p006 22 | CCTCTAGAGT 23 | + 24 | ++++++++++ 25 | @ref1_grp2_p001 26 | AGCTCGGTAC 27 | + 28 | """""""""" 29 | @ref1_grp2_p002 30 | CGGTACCCGG 31 | + 32 | $$$$$$$$$$ 33 | @ref1_grp2_p003 34 | ACCCGGGGAT 35 | + 36 | &&&&&&&&&& 37 | @ref1_grp2_p004 38 | GGGGATCCTC 39 | + 40 | (((((((((( 41 | @ref1_grp2_p005 42 | ATCCTCTAGA 43 | + 44 | ********** 45 | @ref1_grp2_p006 46 | TCTAGAGTCG 47 | + 48 | ,,,,,,,,,, 49 | @ref2_grp3_p001 50 | GTGACACTATAGAAT 51 | + 52 | ~~~~~~~~~~~~~~~ 53 | @ref2_grp3_p002 54 | CTGTTTCCTGTGTGA 55 | + 56 | {{{{{{{{{{{{{{{ 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | TGCAGGCATG 63 | + 64 | AAAAAAAAAA 65 | @ref12_grp2_p001 66 | CAAGCTTGAG 67 | + 68 | AAAAAAAAAA 69 | @unaligned_grp3_p001 70 | CACTCGTTCATGACG 71 | + 72 | 0123456789abcde 73 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/1.2.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | GTCGACTCTA 3 | + 4 | ---------- 5 | @ref1_grp1_p002 6 | GCAGGTCGAC 7 | + 8 | ////////// 9 | @ref1_grp1_p003 10 | GCCTGCAGGT 11 | + 12 | 1111111111 13 | @ref1_grp1_p004 14 | GCATGCCTGC 15 | + 16 | 3333333333 17 | @ref1_grp1_p005 18 | GCTTGCATGC 19 | + 20 | 5555555555 21 | @ref1_grp1_p006 22 | TCAAGCTTGC 23 | + 24 | 7777777777 25 | @ref1_grp2_p001 26 | AGGTCGACTC 27 | + 28 | .......... 29 | @ref1_grp2_p002 30 | CTGCAGGTCG 31 | + 32 | 0000000000 33 | @ref1_grp2_p003 34 | ATGCCTGCAG 35 | + 36 | 2222222222 37 | @ref1_grp2_p004 38 | TTGCATGCCT 39 | + 40 | 4444444444 41 | @ref1_grp2_p005 42 | AAGCTTGCAT 43 | + 44 | 6666666666 45 | @ref1_grp2_p006 46 | ACTCAAGCTT 47 | + 48 | 8888888888 49 | @ref2_grp3_p001 50 | CTGTTTCCTGTGTGA 51 | + 52 | ||||||||||||||| 53 | @ref2_grp3_p002 54 | CGCCAAGCTATTTAG 55 | + 56 | }}}}}}}}}}}}}}} 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | CACTATAGAA 63 | + 64 | BBBBBBBBBB 65 | @ref12_grp2_p001 66 | ATTTAGGTGA 67 | + 68 | BBBBBBBBBB 69 | @unaligned_grp3_p001 70 | GAAAGTGAGGAGGTG 71 | + 72 | edcba9876543210 73 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/1.stdout.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/bam2fq/1.stdout.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/2.1.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | CGAGCTCGGT 3 | + 4 | !!!!!!!!!! 5 | @ref1_grp1_p002 6 | CTCGGTACCC 7 | + 8 | ########## 9 | @ref1_grp1_p003 10 | GTACCCGGGG 11 | + 12 | %%%%%%%%%% 13 | @ref1_grp1_p004 14 | CCGGGGATCC 15 | + 16 | '''''''''' 17 | @ref1_grp1_p005 18 | GGATCCTCTA 19 | + 20 | )))))))))) 21 | @ref1_grp1_p006 22 | CCTCTAGAGT 23 | + 24 | ++++++++++ 25 | @ref1_grp2_p001 26 | AGCTCGGTAC 27 | + 28 | """""""""" 29 | @ref1_grp2_p002 30 | CGGTACCCGG 31 | + 32 | $$$$$$$$$$ 33 | @ref1_grp2_p003 34 | ACCCGGGGAT 35 | + 36 | &&&&&&&&&& 37 | @ref1_grp2_p004 38 | GGGGATCCTC 39 | + 40 | (((((((((( 41 | @ref1_grp2_p005 42 | ATCCTCTAGA 43 | + 44 | ********** 45 | @ref1_grp2_p006 46 | TCTAGAGTCG 47 | + 48 | ,,,,,,,,,, 49 | @ref2_grp3_p001 50 | GTGACACTATAGAAT 51 | + 52 | ~~~~~~~~~~~~~~~ 53 | @ref2_grp3_p002 54 | CTGTTTCCTGTGTGA 55 | + 56 | {{{{{{{{{{{{{{{ 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | TGCAGGCATG 63 | + 64 | AAAAAAAAAA 65 | @ref12_grp2_p001 66 | CAAGCTTGAG 67 | + 68 | AAAAAAAAAA 69 | @unaligned_grp3_p001 70 | CACTCGTTCATGACG 71 | + 72 | 0123456789abcde 73 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/2.2.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | GTCGACTCTA 3 | + 4 | ---------- 5 | @ref1_grp1_p002 6 | GCAGGTCGAC 7 | + 8 | ////////// 9 | @ref1_grp1_p003 10 | GCCTGCAGGT 11 | + 12 | 1111111111 13 | @ref1_grp1_p004 14 | GCATGCCTGC 15 | + 16 | 3333333333 17 | @ref1_grp1_p005 18 | GCTTGCATGC 19 | + 20 | 5555555555 21 | @ref1_grp1_p006 22 | TCAAGCTTGC 23 | + 24 | 7777777777 25 | @ref1_grp2_p001 26 | AGGTCGACTC 27 | + 28 | .......... 29 | @ref1_grp2_p002 30 | CTGCAGGTCG 31 | + 32 | 0000000000 33 | @ref1_grp2_p003 34 | ATGCCTGCAG 35 | + 36 | 2222222222 37 | @ref1_grp2_p004 38 | TTGCATGCCT 39 | + 40 | 4444444444 41 | @ref1_grp2_p005 42 | AAGCTTGCAT 43 | + 44 | 6666666666 45 | @ref1_grp2_p006 46 | ACTCAAGCTT 47 | + 48 | 8888888888 49 | @ref2_grp3_p001 50 | CTGTTTCCTGTGTGA 51 | + 52 | ||||||||||||||| 53 | @ref2_grp3_p002 54 | CGCCAAGCTATTTAG 55 | + 56 | }}}}}}}}}}}}}}} 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | CACTATAGAA 63 | + 64 | BBBBBBBBBB 65 | @ref12_grp2_p001 66 | ATTTAGGTGA 67 | + 68 | BBBBBBBBBB 69 | @unaligned_grp3_p001 70 | GAAAGTGAGGAGGTG 71 | + 72 | edcba9876543210 73 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/2.s.fq.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/bam2fq/2.s.fq.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/2.stdout.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/bam2fq/2.stdout.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/3.1.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | CGAGCTCGGT 3 | + 4 | !!!!!!!!!! 5 | @ref1_grp1_p002 6 | CTCGGTACCC 7 | + 8 | ########## 9 | @ref1_grp1_p003 10 | GTACCCGGGG 11 | + 12 | %%%%%%%%%% 13 | @ref1_grp1_p004 14 | CCGGGGATCC 15 | + 16 | '''''''''' 17 | @ref1_grp1_p005 18 | GGATCCTCTA 19 | + 20 | )))))))))) 21 | @ref1_grp1_p006 22 | CCTCTAGAGT 23 | + 24 | ++++++++++ 25 | @ref1_grp2_p001 26 | AGCTCGGTAC 27 | + 28 | """""""""" 29 | @ref1_grp2_p002 30 | CGGTACCCGG 31 | + 32 | $$$$$$$$$$ 33 | @ref1_grp2_p003 34 | ACCCGGGGAT 35 | + 36 | &&&&&&&&&& 37 | @ref1_grp2_p004 38 | GGGGATCCTC 39 | + 40 | (((((((((( 41 | @ref1_grp2_p005 42 | ATCCTCTAGA 43 | + 44 | ********** 45 | @ref1_grp2_p006 46 | TCTAGAGTCG 47 | + 48 | ,,,,,,,,,, 49 | @ref2_grp3_p001 50 | GTGACACTATAGAAT 51 | + 52 | ~~~~~~~~~~~~~~~ 53 | @ref2_grp3_p002 54 | CTGTTTCCTGTGTGA 55 | + 56 | {{{{{{{{{{{{{{{ 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | TGCAGGCATG 63 | + 64 | AAAAAAAAAA 65 | @ref12_grp2_p001 66 | CAAGCTTGAG 67 | + 68 | AAAAAAAAAA 69 | @unaligned_grp3_p001 70 | CACTCGTTCATGACG 71 | + 72 | 0123456789abcde 73 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/3.2.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | GTCGACTCTA 3 | + 4 | ---------- 5 | @ref1_grp1_p002 6 | GCAGGTCGAC 7 | + 8 | ////////// 9 | @ref1_grp1_p003 10 | GCCTGCAGGT 11 | + 12 | 1111111111 13 | @ref1_grp1_p004 14 | GCATGCCTGC 15 | + 16 | 3333333333 17 | @ref1_grp1_p005 18 | GCTTGCATGC 19 | + 20 | 5555555555 21 | @ref1_grp1_p006 22 | TCAAGCTTGC 23 | + 24 | 7777777777 25 | @ref1_grp2_p001 26 | AGGTCGACTC 27 | + 28 | .......... 29 | @ref1_grp2_p002 30 | CTGCAGGTCG 31 | + 32 | 0000000000 33 | @ref1_grp2_p003 34 | ATGCCTGCAG 35 | + 36 | 2222222222 37 | @ref1_grp2_p004 38 | TTGCATGCCT 39 | + 40 | 4444444444 41 | @ref1_grp2_p005 42 | AAGCTTGCAT 43 | + 44 | 6666666666 45 | @ref1_grp2_p006 46 | ACTCAAGCTT 47 | + 48 | 8888888888 49 | @ref2_grp3_p001 50 | CTGTTTCCTGTGTGA 51 | + 52 | ||||||||||||||| 53 | @ref2_grp3_p002 54 | CGCCAAGCTATTTAG 55 | + 56 | }}}}}}}}}}}}}}} 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | CACTATAGAA 63 | + 64 | BBBBBBBBBB 65 | @ref12_grp2_p001 66 | ATTTAGGTGA 67 | + 68 | BBBBBBBBBB 69 | @unaligned_grp3_p001 70 | GAAAGTGAGGAGGTG 71 | + 72 | edcba9876543210 73 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/3.s.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp2_p002a 2 | CGGTACCCGG 3 | + 4 | $$$$$$$$$$ 5 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/3.stdout.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/bam2fq/3.stdout.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/4.1.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | CGAGCTCGGT 3 | + 4 | !!!!!!!!!! 5 | @ref1_grp1_p002 6 | CTCGGTACCC 7 | + 8 | ########## 9 | @ref1_grp1_p003 10 | GTACCCGGGG 11 | + 12 | %%%%%%%%%% 13 | @ref1_grp1_p004 14 | CCGGGGATCC 15 | + 16 | '''''''''' 17 | @ref1_grp1_p005 18 | GGATCCTCTA 19 | + 20 | )))))))))) 21 | @ref1_grp1_p006 22 | CCTCTAGAGT 23 | + 24 | ++++++++++ 25 | @ref1_grp2_p001 26 | AGCTCGGTAC 27 | + 28 | """""""""" 29 | @ref1_grp2_p002 30 | CGGTACCCGG 31 | + 32 | $$$$$$$$$$ 33 | @ref1_grp2_p003 34 | ACCCGGGGAT 35 | + 36 | &&&&&&&&&& 37 | @ref1_grp2_p004 38 | GGGGATCCTC 39 | + 40 | (((((((((( 41 | @ref1_grp2_p005 42 | ATCCTCTAGA 43 | + 44 | ********** 45 | @ref1_grp2_p006 46 | TCTAGAGTCG 47 | + 48 | ,,,,,,,,,, 49 | @ref2_grp3_p001 50 | GTGACACTATAGAAT 51 | + 52 | ~~~~~~~~~~~~~~~ 53 | @ref2_grp3_p002 54 | CTGTTTCCTGTGTGA 55 | + 56 | {{{{{{{{{{{{{{{ 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | TGCAGGCATG 63 | + 64 | AAAAAAAAAA 65 | @ref12_grp2_p001 66 | CAAGCTTGAG 67 | + 68 | AAAAAAAAAA 69 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/4.2.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp1_p001 2 | GTCGACTCTA 3 | + 4 | ---------- 5 | @ref1_grp1_p002 6 | GCAGGTCGAC 7 | + 8 | ////////// 9 | @ref1_grp1_p003 10 | GCCTGCAGGT 11 | + 12 | 1111111111 13 | @ref1_grp1_p004 14 | GCATGCCTGC 15 | + 16 | 3333333333 17 | @ref1_grp1_p005 18 | GCTTGCATGC 19 | + 20 | 5555555555 21 | @ref1_grp1_p006 22 | TCAAGCTTGC 23 | + 24 | 7777777777 25 | @ref1_grp2_p001 26 | AGGTCGACTC 27 | + 28 | .......... 29 | @ref1_grp2_p002 30 | CTGCAGGTCG 31 | + 32 | 0000000000 33 | @ref1_grp2_p003 34 | ATGCCTGCAG 35 | + 36 | 2222222222 37 | @ref1_grp2_p004 38 | TTGCATGCCT 39 | + 40 | 4444444444 41 | @ref1_grp2_p005 42 | AAGCTTGCAT 43 | + 44 | 6666666666 45 | @ref1_grp2_p006 46 | ACTCAAGCTT 47 | + 48 | 8888888888 49 | @ref2_grp3_p001 50 | CTGTTTCCTGTGTGA 51 | + 52 | ||||||||||||||| 53 | @ref2_grp3_p002 54 | CGCCAAGCTATTTAG 55 | + 56 | }}}}}}}}}}}}}}} 57 | @ref2_grp3_p003 58 | ACGTMRWSYKVHDBN 59 | + 60 | 0123456789abcd! 61 | @ref12_grp1_p001 62 | CACTATAGAA 63 | + 64 | BBBBBBBBBB 65 | @ref12_grp2_p001 66 | ATTTAGGTGA 67 | + 68 | BBBBBBBBBB 69 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/4.s.fq.expected: -------------------------------------------------------------------------------- 1 | @ref1_grp2_p002a 2 | CGGTACCCGG 3 | + 4 | $$$$$$$$$$ 5 | @unaligned_grp3_p001 6 | CACTCGTTCATGACG 7 | + 8 | 0123456789abcde 9 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/bam2fq/4.stdout.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/bam2fq/4.stdout.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/cat.hdr: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @RG ID:g1 DS:Group 1 LB:Lib1 SM:Sample1 3 | @PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 4 | @CO The MIT License 5 | @CO 6 | @CO Copyright (c) 2014 Genome Research Ltd. 7 | @CO 8 | @CO Permission is hereby granted, free of charge, to any person obtaining a copy 9 | @CO of this software and associated documentation files (the "Software"), to deal 10 | @CO in the Software without restriction, including without limitation the rights 11 | @CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | @CO copies of the Software, and to permit persons to whom the Software is 13 | @CO furnished to do so, subject to the following conditions: 14 | @CO 15 | @CO The above copyright notice and this permission notice shall be included in 16 | @CO all copies or substantial portions of the Software. 17 | @CO 18 | @CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | @CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | @CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | @CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | @CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | @CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 24 | @CO THE SOFTWARE. 25 | @SQ SN:ref1 LN:10000 26 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468: -------------------------------------------------------------------------------- 1 | CGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGAGT 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437: -------------------------------------------------------------------------------- 1 | ATTCTATAGTGTCACCTAAATAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGA 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4: -------------------------------------------------------------------------------- 1 | GGGATCCTCTAGAGT*****CGACCTGCAGGCATG 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b: -------------------------------------------------------------------------------- 1 | GGGATCCTCTAGAGTCGACCTGCAGGCATG 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/depad.001.fa: -------------------------------------------------------------------------------- 1 | >ref1 2 | GGGATCCTCTAGAGT*****CGACCTGCAGGCATG 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/depad.001.fa.fai: -------------------------------------------------------------------------------- 1 | ref1 35 6 35 36 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/dict.fa: -------------------------------------------------------------------------------- 1 | >chr1 2 | TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC 3 | TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA 4 | A 5 | >chr2 6 | CATCTCTACAAGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATAC 7 | TTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTTGACACCTTT 8 | T 9 | >chr3 10 | CGTATGCGCTTTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAAT 11 | AAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGGAATGTGCAA 12 | A 13 | >chr4 14 | CGTGATACCAACTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATAT 15 | TTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGGTTTGCAGCC 16 | C 17 | >chr5 18 | NTCTCATTTAAAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTT 19 | CATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCAAGACGTTATC 20 | T 21 | >chr6 22 | NAATTGTTCTTAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACA 23 | ATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACCAGTGTCGAT 24 | C 25 | >chr7 26 | CAACAGAAGGGGGGATCTGTGTTTGTGTTTCGGATTTCCTGCTGAAAAGG 27 | TTTTCGGGTCCCCCCCCCATCCCGATTTCCTTCCGCAGCTTACCTCCCGA 28 | AACGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCA 29 | GCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCCAGAGCATA 30 | CACAACAGAAGGGGGGATCTGTGTTTGTGTTTCGGATTTCCTGCTGAAAA 31 | GGTTTTCGGGTCCCCCCCCCATCCCGATTTCCTTCCGCAGCTTACCTCCC 32 | GAAACGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGG 33 | CAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCCAGAGCA 34 | TACA 35 | >chr8 36 | CACATCGTGAATCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGA 37 | GAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCCTAAGATGAC 38 | CCCAGGTTCAAATGTGCAGCCCCTTTTGAGAGATTTTTTTTTTGGGCTGG 39 | AAAAAAGACACAGCTATTCCTAAGATGACAAGATCAGAAAAAAAGTCAAG 40 | CA 41 | >chr8:lower 42 | cacatcgtgaatcttacaatctgcggtttcagatgtggagcgatgtgtga 43 | gagattgagcaactgatctgaaaagcagacacagctattcctaagatgac 44 | cccaggttcaaatgtgcagccccttttgagagattttttttttgggctgg 45 | aaaaaagacacagctattcctaagatgacaagatcagaaaaaaagtcaag 46 | ca 47 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/dict.out: -------------------------------------------------------------------------------- 1 | @HD VN:1.0 SO:unsorted 2 | @SQ SN:chr1 LN:101 M5:bd01f7e11515bb6beda8f7257902aa67 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 3 | @SQ SN:chr2 LN:101 M5:31c33e2155b3de5e2554b693c475b310 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 4 | @SQ SN:chr3 LN:101 M5:631593c6dd2048ae88dcce2bd505d295 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 5 | @SQ SN:chr4 LN:101 M5:c60cb92f1ee5b78053c92bdbfa19abf1 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 6 | @SQ SN:chr5 LN:101 M5:07ebc213c7611db0eacbb1590c3e9bda UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 7 | @SQ SN:chr6 LN:101 M5:7be2f5e7ee39e60a6c3b5b6a41178c6d UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 8 | @SQ SN:chr7 LN:404 M5:da488fc432cdaf2c20c96da473a7b630 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 9 | @SQ SN:chr8 LN:202 M5:d339678efce576d5546e88b49a487b63 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 10 | @SQ SN:chr8:lower LN:202 M5:d339678efce576d5546e88b49a487b63 UR:ftp://orthanc.org/hf37d5.fa.gz AS:hf37d5 SP:Homo floresiensis 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/empty.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/dat/empty.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/large_chrom.out: -------------------------------------------------------------------------------- 1 | ref2_grp3_p001 83 ref2 1 99 15M = 31 45 ATTCTATAGTGTCAC ~~~~~~~~~~~~~~~ RG:Z:grp3 NM:i:0 MD:Z:15 2 | ref12_grp1_p001 145 ref2 2 50 10M ref1 36 0 TTCTATAGTG BBBBBBBBBB RG:Z:grp1 NM:i:0 MD:Z:10 3 | ref12_grp2_p001 145 ref2 12 50 10M ref1 46 0 TCACCTAAAT BBBBBBBBBB RG:Z:grp2 NM:i:0 MD:Z:10 4 | ref2_grp3_p002 147 ref2 436870911 99 15M = 46 45 CTAAATAGCTTGGCG }}}}}}}}}}}}}}} RG:Z:grp3 NM:i:0 MD:Z:15 5 | ref2_grp3_p001 163 ref2 536880911 99 15M = 1 -45 CTGTTTCCTGTGTGA ||||||||||||||| RG:Z:grp3 NM:i:13 MD:Z:0T0A0A1C0A0T0G0G0T0C0A1A0G0 6 | ref2_grp3_p002 99 ref2 541556280 99 15M = 16 -45 CTGTTTCCTGTGTGA {{{{{{{{{{{{{{{ RG:Z:grp3 NM:i:0 MD:Z:15 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/large_chrom_bai_index.err: -------------------------------------------------------------------------------- 1 | [Error] chromosome too large for BAI index. Try CSI index with `samtools index -c` instead. 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/mpileup.err.1: -------------------------------------------------------------------------------- 1 | [mpileup] 3 samples in 3 input files 2 | Set max per-file depth to 2666 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/mpileup.out.3: -------------------------------------------------------------------------------- 1 | 17 1050 A 6 .$..... DGIKIF 2 | 17 1051 A 5 ..... HFJHD 3 | 17 1052 A 5 ..... BIKJB 4 | 17 1053 A 5 ..... GFJGB 5 | 17 1054 C 5 ..... I@JHB 6 | 17 1055 C 7 .....^].^]. HKNK9@A 7 | 17 1056 C 7 ....... HKMK7A@ 8 | 17 1057 T 7 ....... JDKJDGF 9 | 17 1058 G 7 ....... HHLKHIH 10 | 17 1059 T 7 ....... EHII?EE 11 | 17 1060 C 7 ....... JJJI=GH 12 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/mpileup.ref.fa.fai: -------------------------------------------------------------------------------- 1 | 17 4200 14 60 61 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_a.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/dat/test_input_1_a.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_a.bam.bai.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/dat/test_input_1_a.bam.bai.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_a.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:insert LN:599 3 | @SQ SN:ref1 LN:45 4 | @SQ SN:ref2 LN:40 5 | @SQ SN:ref3 LN:4 6 | @RG ID:fish PG:donkey 7 | @RG ID:cow PU:13_&^&&*(:332 8 | @RG PU:*9u8jkjjkjd: ID:colt 9 | @PG ID:bull PP:donkey 10 | @PG ID:donkey 11 | @PG ID:moose 12 | @PG PP:moose ID:cow 13 | @CO 14 | r000 99 insert 50 30 10M = 80 30 ATTTAGCTAC AAAAAAAAAA RG:Z:cow PG:Z:bull 15 | r000 211 insert 80 30 10M = 50 -30 CCCAATCATT AAAAAAAAAA RG:Z:cow PG:Z:bull 16 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:fish PG:Z:colt 17 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 PG:Z:colt 18 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:cow 19 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:colt 20 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:cow PG:Z:colt 21 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:fish PG:Z:colt 22 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:colt PG:Z:bull 23 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:colt PG:Z:bull 24 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:fish PG:Z:bull 25 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:fish PG:Z:bull 26 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:fish PG:Z:bull 27 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow 28 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAAAAAAAA ??????????????????????? 29 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_a_regex.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:insert LN:599 3 | @SQ SN:ref1|this=that LN:45 4 | @SQ SN:ref2*HLA:1a:2:b LN:40 5 | @SQ SN:ref3 LN:4 6 | @RG ID:fish PG:donkey 7 | @RG ID:cow PU:13_&^&&*(:332 8 | @RG PU:*9u8jkjjkjd: ID:colt 9 | @PG ID:bull PP:donkey 10 | @PG ID:donkey 11 | @PG ID:moose 12 | @PG PP:moose ID:cow 13 | @CO 14 | r000 99 insert 50 30 10M = 80 30 ATTTAGCTAC AAAAAAAAAA RG:Z:cow PG:Z:bull 15 | r000 211 insert 80 30 10M = 50 -30 CCCAATCATT AAAAAAAAAA RG:Z:cow PG:Z:bull 16 | r001 163 ref1|this=that 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:fish PG:Z:colt 17 | r002 0 ref1|this=that 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 PG:Z:colt 18 | r003 0 ref1|this=that 9 30 5H6M * 0 0 AGCTAA * RG:Z:cow 19 | r004 0 ref1|this=that 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:colt 20 | r003 16 ref1|this=that 29 30 6H5M * 0 0 TAGGC * RG:Z:cow PG:Z:colt 21 | r001 83 ref1|this=that 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:fish PG:Z:colt 22 | x1 0 ref2*HLA:1a:2:b 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:colt PG:Z:bull 23 | x2 0 ref2*HLA:1a:2:b 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:colt PG:Z:bull 24 | x3 0 ref2*HLA:1a:2:b 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:fish PG:Z:bull 25 | x4 0 ref2*HLA:1a:2:b 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:fish PG:Z:bull 26 | x5 0 ref2*HLA:1a:2:b 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:fish PG:Z:bull 27 | x6 0 ref2*HLA:1a:2:b 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow 28 | u1 4 * 0 30 23M * 0 0 TAATTAAGTCTACAGAAAAAAAA ??????????????????????? 29 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_b.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/dat/test_input_1_b.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_b.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:insert LN:599 3 | @SQ SN:ref1 LN:45 4 | @SQ SN:ref2 LN:40 5 | @SQ SN:ref3 LN:4 6 | @PG ID:llama 7 | @RG ID:fish PG:llama 8 | @RG ID:cow PU:13_&^&&*(:332 PG:donkey 9 | @RG PU:*9u8jkjjkjd: ID:colt 10 | @PG ID:bull PP:donkey 11 | @PG ID:donkey 12 | @CO Do you know? 13 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:colt PG:Z:donkey 14 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:colt PG:Z:donkey 15 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:colt PG:Z:donkey 16 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:donkey 17 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:colt PG:Z:donkey 18 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:colt PG:Z:donkey 19 | x7 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:cow PG:Z:bull 20 | x8 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:cow PG:Z:bull 21 | x9 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:cow PG:Z:bull 22 | x10 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:cow PG:Z:bull 23 | x11 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:cow PG:Z:bull 24 | x12 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow PG:Z:bull 25 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_b_regex.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:insert LN:599 3 | @SQ SN:ref2*HLA:1a:2:b LN:40 4 | @SQ SN:ref3 LN:4 5 | @SQ SN:ref1 LN:45 6 | @PG ID:llama_{a} 7 | @RG ID:fish-[1] PG:llama_{a} 8 | @RG ID:cow-[2] PU:13_&^&&*(:332 PG:donkey 9 | @RG PU:*9u8jkjjkjd: ID:colt 10 | @PG ID:bull PP:donkey 11 | @PG ID:donkey 12 | @CO Do you know? 13 | x7 0 ref2*HLA:1a:2:b 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:cow-[2] PG:Z:bull 14 | x8 0 ref2*HLA:1a:2:b 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:cow-[2] PG:Z:bull 15 | x9 0 ref2*HLA:1a:2:b 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:cow-[2] PG:Z:bull 16 | x10 0 ref2*HLA:1a:2:b 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:cow-[2] PG:Z:bull 17 | x11 0 ref2*HLA:1a:2:b 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:cow-[2] PG:Z:bull 18 | x12 0 ref2*HLA:1a:2:b 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow-[2] PG:Z:bull 19 | r005 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:colt PG:Z:donkey 20 | r006 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:colt PG:Z:donkey 21 | r007 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:colt PG:Z:donkey 22 | r007 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:donkey 23 | r006 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:colt PG:Z:donkey 24 | r005 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:colt PG:Z:donkey 25 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_c.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/dat/test_input_1_c.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/test_input_1_c.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | @RG ID:fish 5 | @RG ID:cow PU:13_&^&&*(:332 6 | @RG PU:*9u8jkjjkjd: ID:colt 7 | @PG ID:bull PP:donkey 8 | @PG ID:donkey 9 | @CO Do you know? 10 | @CO Another comment from test_input_1_c 11 | r008 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:colt PG:Z:donkey 12 | r009 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 RG:Z:colt PG:Z:donkey 13 | r010 0 ref1 9 30 5H6M * 0 0 AGCTAA * RG:Z:colt PG:Z:donkey 14 | r010 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * RG:Z:colt PG:Z:donkey 15 | r009 16 ref1 29 30 6H5M * 0 0 TAGGC * RG:Z:colt PG:Z:donkey 16 | r008 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:colt PG:Z:donkey 17 | x10 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * RG:Z:cow PG:Z:bull 18 | x11 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? RG:Z:cow PG:Z:bull 19 | x12 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? RG:Z:cow PG:Z:bull 20 | x13 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? RG:Z:cow PG:Z:bull 21 | x14 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? RG:Z:cow PG:Z:bull 22 | x15 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? RG:Z:cow PG:Z:bull 23 | u2 4 * 0 30 * * 0 0 TAATTAAGTCTACAGAAAAAAAA ??????????????????????? 24 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.001.01.bed: -------------------------------------------------------------------------------- 1 | # The MIT License 2 | # 3 | # Copyright (c) 2014 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 | browser position ref1:1-56 23 | browser hide all 24 | track name="my track" description="A track line" visibility=2 colorByStrand="255,0,0 0,0,255" 25 | ref1 10 24 somewhere 500 + 10 24 127,127,0 2 2,2 10,22 26 | ref1 44 45 27 | ref2 16 28 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.001.02.bed: -------------------------------------------------------------------------------- 1 | # The MIT License 2 | # 3 | # Copyright (c) 2014 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 | ref1 5 20 23 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.001.fa: -------------------------------------------------------------------------------- 1 | >ref1 2 | CGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGAGT 3 | >ref2 4 | ATTCTATAGTGTCACCTAAATAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGA 5 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.001.fa.fai: -------------------------------------------------------------------------------- 1 | ref1 56 6 56 57 2 | ref2 60 69 60 61 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.002.01.bed: -------------------------------------------------------------------------------- 1 | # The MIT License 2 | # 3 | # Copyright (c) 2014 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 | browser position ref1:1-56 23 | browser hide all 24 | track name="my track" description="A track line" visibility=2 colorByStrand="255,0,0 0,0,255" 25 | Z 19 40 somewhere 500 + 20 40 127,127,0 2 2,2 10,22 26 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.002.02.bed: -------------------------------------------------------------------------------- 1 | # The MIT License 2 | # 3 | # Copyright (c) 2014 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 | browser position ref1:1-56 23 | browser hide all 24 | track name="my track" description="A track line" visibility=2 colorByStrand="255,0,0 0,0,255" 25 | Z 9 15 26 | Z 20 27 | Z 24 30 28 | Z 35 29 | Z 39 45 30 | Z 42 50 31 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.002.fa: -------------------------------------------------------------------------------- 1 | >Z 2 | TAGGACATGTACACTCGTTCATGACGTCTTGTCTATACGAAAGTGAGGAGGTGTAGTCAT 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.002.fa.fai: -------------------------------------------------------------------------------- 1 | Z 60 3 60 61 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/dat/view.003.expected.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample 3 | @PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 4 | @CO The MIT License 5 | @CO 6 | @CO Copyright (c) 2014 Genome Research Ltd. 7 | @CO 8 | @CO Permission is hereby granted, free of charge, to any person obtaining a copy 9 | @CO of this software and associated documentation files (the "Software"), to deal 10 | @CO in the Software without restriction, including without limitation the rights 11 | @CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 12 | @CO copies of the Software, and to permit persons to whom the Software is 13 | @CO furnished to do so, subject to the following conditions: 14 | @CO 15 | @CO The above copyright notice and this permission notice shall be included in 16 | @CO all copies or substantial portions of the Software. 17 | @CO 18 | @CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 19 | @CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 20 | @CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 21 | @CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 22 | @CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 23 | @CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 24 | @CO THE SOFTWARE. 25 | @CO 26 | @CO Test file for the -B option. Only very basic tests here. The full 27 | @CO B operator semantics are currently not well defined so it's not 28 | @CO possible to say what should happen in certain cases. 29 | @CO For a long discussion of B operators, see 30 | @CO https://sourceforge.net/p/samtools/mailman/message/28463294/ 31 | @CO 32 | @SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 33 | ref1_grp1_p001 0 ref1 1 0 15M = 25 34 CGAGCACGGTACCCG AAAAA"BBBBBBBBB RG:Z:grp1 34 | ref1_grp1_p002 0 ref1 1 0 15M = 25 34 CGAGCTCGGTACCCG BBBBB"BBBBAAAAA RG:Z:grp1 35 | ref1_grp1_p003 0 ref1 1 0 15M = 25 34 CGAGCACGGTACCCG 000002AAAAAAAAA RG:Z:grp1 36 | ref1_grp1_p004 0 ref1 1 0 15M = 25 34 CGAGCTCGGTACCCG AAAAA2AAAA00000 RG:Z:grp1 37 | ref1_grp1_p005 4 ref1 2 0 1M2B1M = 25 34 GC AA RG:Z:grp1 38 | ref1_grp1_p006 0 ref1 2 0 1M1I1M = 25 34 GTA 0AA RG:Z:grp1 39 | ref1_grp1_p007 0 ref1 3 0 1M1D1M = 25 34 AG 00 RG:Z:grp1 40 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/1_coord_sort.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 5 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 6 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * 7 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 8 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * 9 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 10 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 11 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 12 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 13 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 14 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 15 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 16 | u1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? 17 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/1_coord_sort.sam.expected: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/fixmate/1_coord_sort.sam.expected -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/1_coord_sort.sam.expected.err: -------------------------------------------------------------------------------- 1 | [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. 2 | 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/2_isize_overflow.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | of1 99 ref1 10 30 23M = 8 2 AAGTCGGCAGCGTCAGATGTGTA ??????????????????????? 5 | of1 147 ref1 8 30 23M = 10 -2 CTGTCTCTTATACACATCTCCTT ??????????????????????? 6 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * 7 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 9 | r003 0 ref1 9 30 5H6M * 0 0 AGCTAA * 10 | r003 16 ref1 29 30 6H5M * 0 0 TAGGC * 11 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 12 | u1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? 13 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 14 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 15 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 16 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 17 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 18 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 19 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/2_isize_overflow.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:ref1 LN:45 3 | @SQ SN:ref2 LN:40 4 | of1 99 ref1 10 30 23M = 8 21 AAGTCGGCAGCGTCAGATGTGTA ??????????????????????? MQ:i:30 5 | of1 147 ref1 8 30 23M = 10 -21 CTGTCTCTTATACACATCTCCTT ??????????????????????? MQ:i:30 6 | r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * MQ:i:30 7 | r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 MQ:i:30 8 | r002 0 ref1 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * XA:Z:abc XB:i:-10 9 | r003 33 ref1 9 30 5H6M = 29 25 AGCTAA * MQ:i:30 10 | r003 17 ref1 29 30 6H5M = 9 -25 TAGGC * MQ:i:30 11 | r004 0 ref1 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * 12 | u1 4 * 0 30 * * 0 0 TAATTGGGTCTTCAGAGCACCTA ??????????????????????? 13 | x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA * 14 | x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? 15 | x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? 16 | x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? 17 | x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? 18 | x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? 19 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/3_reverse_read_pp_lt.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40340 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U 5 | MS0_12500:1:2114:20577:3664#6 147 1 40340 23 75M = 40346 -75 CAAAATCTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/3_reverse_read_pp_lt.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40340 69 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 5 | MS0_12500:1:2114:20577:3664#6 147 1 40340 23 75M = 40346 -69 CAAAATCTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/4_reverse_read_pp_equal.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U 5 | MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/4_reverse_read_pp_equal.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 5 | MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/5_ct.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U 5 | MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 MQ:i:23 XT:A:U 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/5_ct.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 ct:Z:1F75M-75T2R75M 5 | MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/6_ct_replace.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 5 | MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 ct:Z:1F70M-75T2R70M 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/fixmate/6_ct_replace.sam.expected: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:queryname 2 | @SQ SN:1 LN:4569345 3 | @RG ID:1#6 LB:1 SM:a 4 | MS0_12500:1:2114:20577:3664#6 99 1 40346 23 75M = 40346 75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD X0:i:1 X1:i:1 XA:Z:X,+8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 ct:Z:1F75M-75T2R75M 5 | MS0_12500:1:2114:20577:3664#6 147 1 40346 23 75M = 40346 -75 CTCATGGACACCAACCACTCAATTATCTATCCACCTAGCCATGGCCATCACCTTATGAGCGGGCGCAGTGACTAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFCCF@GGGGGGGGGCCCCC X0:i:1 X1:i:1 XA:Z:X,-8796,75M,2; MD:Z:22C52 RG:Z:1#6 XG:i:0 AM:i:23 NM:i:1 SM:i:23 XM:i:1 XO:i:0 XT:A:U MQ:i:23 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/idxstats/test_input_1_a.bam.expected: -------------------------------------------------------------------------------- 1 | insert 599 2 0 2 | ref1 45 6 0 3 | ref2 40 6 0 4 | ref3 4 0 0 5 | * 0 0 1 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/idxstats/test_input_1_a.bam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/idxstats/test_input_1_a.bam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/2.merge.expected.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/merge/2.merge.expected.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/3.merge.expected.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/merge/3.merge.expected.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/3.merge.expected.err: -------------------------------------------------------------------------------- 1 | [bam_translate] PG tag "colt" on read "r001" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/4.merge.expected.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/merge/4.merge.expected.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/5.merge.expected.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/merge/5.merge.expected.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/6.merge.expected.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/merge/6.merge.expected.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/7.merge.expected.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/merge/7.merge.expected.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/test_3.fofn: -------------------------------------------------------------------------------- 1 | dat/test_input_1_b.bam 2 | dat/test_input_1_c.bam 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/merge/test_header.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:insert LN:599 3 | @SQ SN:1 LN:45 4 | @SQ SN:2 LN:40 5 | @SQ SN:3 LN:4 6 | @RG ID:fish 7 | @RG ID:cow PU:13_&^&&*(:332 8 | @RG PU:*9u8jkjjkjd: ID:colt 9 | @PG ID:bull PP:donkey 10 | @PG ID:donkey 11 | @CO 12 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/1read.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/1read.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/1read.sam: -------------------------------------------------------------------------------- 1 | @SQ 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/anomalous.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.0 SO:coordinate 2 | @SQ SN:17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human 3 | foo1 99 17 478 60 100M = 478 100 TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGG BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:ERR162872 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 XT:A:U BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 4 | foo1 147 17 478 60 100M = 478 -100 TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGG BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:ERR162872 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 XT:A:U BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 5 | foo2 97 17 478 60 100M = 478 100 TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGG BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:ERR162872 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 XT:A:U BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 6 | foo2 145 17 478 60 100M = 478 -100 TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGG BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:ERR162872 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 XT:A:U BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1#ID.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/c1#ID.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1#ID2.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/c1#ID2.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1#clip.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/c1#clip.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1#pad1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/c1#pad1.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1#pad2.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/c1#pad2.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1#pad3.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/c1#pad3.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1.fa: -------------------------------------------------------------------------------- 1 | >c1 2 | AACCGCGGTT 3 | >c2 4 | CCAATAACC 5 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/c1.fa.fai: -------------------------------------------------------------------------------- 1 | c1 10 4 10 11 2 | c2 7 19 7 8 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#5b.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#5b.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#5b.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#5b.bam.bai -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#5b.cram: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#5b.cram -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#5b.cram.crai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#5b.cram.crai -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#5b.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:15072423 M5:6f60cdf4c739651ae72d53e2e94825c1 2 | @SQ SN:CHROMOSOME_II LN:15279345 M5:73d180d5cb3860a2713927b6812eab0e 3 | @SQ SN:CHROMOSOME_III LN:13783700 M5:0d4dfc45807d6a11439e858605cb364d 4 | @SQ SN:CHROMOSOME_IV LN:17493793 M5:02099b2aad2cfe707759353724fb40ae 5 | @SQ SN:CHROMOSOME_V LN:20924149 M5:6ec590eb82c361a61e6baabce20109bc 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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#large_seq.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#large_seq.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#unmap.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#unmap.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#unmap1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#unmap1.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/ce#unmap2.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/ce#unmap2.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/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 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/depth.reg: -------------------------------------------------------------------------------- 1 | # First field: 2 | # INIT = initialisation, not counted in testing 3 | # P = expected to pass 4 | # F = expected to fail 5 | 6 | # Second field: 7 | # Filename of expected output 8 | 9 | # Third onwards; command to execute. $fmt is replaced by the current file 10 | # format, ie sam, bam or cram. $samtools is a pointer to the desired 11 | # samtools binary. This can be useful for testing older versions. 12 | 13 | # Create indexed BAMs 14 | INIT x $samtools view -b -o xx#depth1.bam xx#depth1.sam 15 | INIT x $samtools view -b -o xx#depth2.bam xx#depth2.sam 16 | INIT x $samtools index xx#depth1.bam 17 | INIT x $samtools index xx#depth2.bam 18 | 19 | # Test basic 1 and 2 file outputs 20 | P d1_1.out $samtools depth xx#depth1.sam 21 | P d1_2.out $samtools depth xx#depth2.sam 22 | P d1_12.out $samtools depth xx#depth1.sam xx#depth2.sam 23 | 24 | # Regions via -r or bed 25 | P d1_12.out $samtools depth -r xx:5-16 xx#depth1.bam xx#depth2.bam 26 | P d1_12.out $samtools depth -b xx.bed xx#depth1.sam xx#depth2.sam 27 | P d2_12r.out $samtools depth -r xx:8-13 xx#depth1.bam xx#depth2.bam 28 | P d2_12r.out $samtools depth -b xx.bed2 xx#depth1.sam xx#depth2.sam 29 | 30 | # With single -a for all (in used refs) 31 | P d3_12r1a.out $samtools depth -a -r xx:5-16 xx#depth1.bam xx#depth2.bam 32 | P d3_12r1a.out $samtools depth -a -b xx.bed xx#depth1.bam xx#depth2.bam 33 | P d3_12r2a.out $samtools depth -a -r xx:8-13 xx#depth1.bam xx#depth2.bam 34 | P d3_12r2a.out $samtools depth -a -b xx.bed2 xx#depth1.bam xx#depth2.bam 35 | 36 | # With double -a for all including unused refs 37 | P d4_12.out $samtools depth -a -a xx#depth1.bam xx#depth2.bam 38 | P d4_12r.out $samtools depth -a -a -r xx:5-16 xx#depth1.bam xx#depth2.bam 39 | P d4_12b.out $samtools depth -a -a -b xx.bed xx#depth1.bam xx#depth2.bam 40 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/10.out: -------------------------------------------------------------------------------- 1 | xx 1 A 1 ^". * 2 | xx 2 A 1 . * 3 | xx 3 A 1 . * 4 | xx 4 A 1 . * 5 | xx 5 A 1 . * 6 | xx 6 A 2 G^"G ** 7 | xx 7 A 2 .. ** 8 | xx 8 A 2 .. ** 9 | xx 9 A 2 .. ** 10 | xx 10 A 2 .. ** 11 | xx 11 T 3 ..^", *** 12 | xx 12 T 3 .., *** 13 | xx 13 T 3 .., *** 14 | xx 14 T 3 .., *** 15 | xx 15 T 3 G$Gg *** 16 | xx 16 T 2 ., ** 17 | xx 17 T 2 ., ** 18 | xx 18 T 2 ., ** 19 | xx 19 T 2 ., ** 20 | xx 20 T 2 G$g ** 21 | xx 21 C 1 , * 22 | xx 22 C 1 , * 23 | xx 23 C 1 , * 24 | xx 24 C 1 , * 25 | xx 25 C 1 ,$ * 26 | yy 1 A 1 ^". * 27 | yy 2 A 1 . * 28 | yy 3 A 1 . * 29 | yy 4 A 1 . * 30 | yy 5 A 1 . * 31 | yy 6 A 2 .^". ** 32 | yy 7 A 2 .. ** 33 | yy 8 A 2 .. ** 34 | yy 9 A 2 .. ** 35 | yy 10 A 2 .$. ** 36 | yy 11 T 1 . * 37 | yy 12 T 1 . * 38 | yy 13 T 1 . * 39 | yy 14 T 1 . * 40 | yy 15 T 1 .$ * 41 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/11.out: -------------------------------------------------------------------------------- 1 | c2 1 C 5 ^!.^!.^!.^!.^!. B~~~~ 2 | c2 2 C 5 ..+3GGG.+1G.-5AATAA.-1A E~~~~ 3 | c2 3 A 5 ...**-3ATA ^~~~~ 4 | c2 4 A 5 ...** \~~~~ 5 | c2 5 T 5 ...** Q~~~~ 6 | c2 6 A 5 ...**-1A @~~~~ 7 | c2 7 A 5 ..+3GGG.+1G** 1~~~~ 8 | c2 8 N 5 CCCCC !~~~~ 9 | c2 9 N 5 C$C$C$C$C$ !~~~~ 10 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/12.out: -------------------------------------------------------------------------------- 1 | c2 1 C 7 ^!.^!.^!.^!.^!.^!.^!. !~~~~~~ 2 | c2 2 C 7 TT-2AAT-2AAT-2AAT-1ATT+3GGG !~~~~~~ 3 | c2 3 A 7 .****.* >~~~~~~ 4 | c2 4 A 7 .**+1G*+2GGC+2GG.+1G* @~~~~~~ 5 | c2 5 T 7 ..-2AA*+1T*+2GTC+2GG*+1A* @~~~~~~ 6 | c2 6 A 7 .***C-1A.* =~~~~~~ 7 | c2 7 A 7 .****.*+3GGT 1~~~~~~ 8 | c2 8 N 7 TTTTTTT !~~~~~~ 9 | c2 9 N 7 C$C$C$C$C$C$C$ !~~~~~~ 10 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/2.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/2.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/26.out: -------------------------------------------------------------------------------- 1 | 17 478 N 2 ^]T^]t BB 2 | 17 479 N 2 Aa CC 3 | 17 480 N 2 Gg GG 4 | 17 481 N 2 Gg >> 5 | 17 482 N 2 Aa EE 6 | 17 483 N 2 Gg GG 7 | 17 484 N 2 Aa 99 8 | 17 485 N 2 Gg GG 9 | 17 486 N 2 Aa GG 10 | 17 487 N 2 Gg II 11 | 17 488 N 2 Aa CC 12 | 17 489 N 2 Aa CC 13 | 17 490 N 2 Aa @@ 14 | 17 491 N 2 Tt ;; 15 | 17 492 N 2 Gg HH 16 | 17 493 N 2 Aa HH 17 | 17 494 N 2 Aa II 18 | 17 495 N 2 Gg LL 19 | 17 496 N 2 Aa II 20 | 17 497 N 2 Cc HH 21 | 17 498 N 2 Aa II 22 | 17 499 N 2 Tt II 23 | 17 500 N 2 Aa CC 24 | 17 501 N 2 Tt FF 25 | 17 502 N 2 Gg EE 26 | 17 503 N 2 Tt KK 27 | 17 504 N 2 Cc JJ 28 | 17 505 N 2 Cc << 29 | 17 506 N 2 Aa 99 30 | 17 507 N 2 Cc JJ 31 | 17 508 N 2 Aa II 32 | 17 509 N 2 Cc 99 33 | 17 510 N 2 Aa II 34 | 17 511 N 2 Aa << 35 | 17 512 N 2 Aa 33 36 | 17 513 N 2 Aa JJ 37 | 17 514 N 2 Aa 77 38 | 17 515 N 2 Cc II 39 | 17 516 N 2 Cc == 40 | 17 517 N 2 Tt EE 41 | 17 518 N 2 Gg KK 42 | 17 519 N 2 Tt BB 43 | 17 520 N 2 Tt DD 44 | 17 521 N 2 Cc FF 45 | 17 522 N 2 Aa ?? 46 | 17 523 N 2 Tt AA 47 | 17 524 N 2 Tt 22 48 | 17 525 N 2 Gg FF 49 | 17 526 N 2 Cc HH 50 | 17 527 N 2 Aa II 51 | 17 528 N 2 Gg KK 52 | 17 529 N 2 Cc 22 53 | 17 530 N 2 Tt BB 54 | 17 531 N 2 Tt FF 55 | 17 532 N 2 Tt FF 56 | 17 533 N 2 Cc JJ 57 | 17 534 N 2 Tt JJ 58 | 17 535 N 2 Aa << 59 | 17 536 N 2 Cc FF 60 | 17 537 N 2 Cc 22 61 | 17 538 N 2 Aa CC 62 | 17 539 N 2 Tt HH 63 | 17 540 N 2 Cc FF 64 | 17 541 N 2 Aa II 65 | 17 542 N 2 Cc GG 66 | 17 543 N 2 Cc JJ 67 | 17 544 N 2 Aa JJ 68 | 17 545 N 2 Aa CC 69 | 17 546 N 2 Aa GG 70 | 17 547 N 2 Aa JJ 71 | 17 548 N 2 Aa JJ 72 | 17 549 N 2 Tt FF 73 | 17 550 N 2 Tt ;; 74 | 17 551 N 2 Gg 88 75 | 17 552 N 2 Cc 33 76 | 17 553 N 2 Aa HH 77 | 17 554 N 2 Aa CC 78 | 17 555 N 2 Aa // 79 | 17 556 N 2 Cc KK 80 | 17 557 N 2 Aa EE 81 | 17 558 N 2 Aa ?? 82 | 17 559 N 2 Cc II 83 | 17 560 N 2 Cc II 84 | 17 561 N 2 Aa 99 85 | 17 562 N 2 Cc II 86 | 17 563 N 2 Aa HH 87 | 17 564 N 2 Cc 00 88 | 17 565 N 2 Gg >> 89 | 17 566 N 2 Cc DD 90 | 17 567 N 2 Cc (( 91 | 17 568 N 2 Cc JJ 92 | 17 569 N 2 Tt 55 93 | 17 570 N 2 Tt EE 94 | 17 571 N 2 Cc @@ 95 | 17 572 N 2 Aa FF 96 | 17 573 N 2 Aa 66 97 | 17 574 N 2 Cc 99 98 | 17 575 N 2 Tt 77 99 | 17 576 N 2 Gg ?? 100 | 17 577 N 2 G$g$ @@ 101 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/29.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/29.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/3.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/3.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/30.out: -------------------------------------------------------------------------------- 1 | 17 478 N 1 ^]T B 2 | 17 479 N 1 A C 3 | 17 480 N 1 G G 4 | 17 481 N 1 G > 5 | 17 482 N 1 A E 6 | 17 483 N 1 G G 7 | 17 484 N 1 A 9 8 | 17 485 N 1 G G 9 | 17 486 N 1 A G 10 | 17 487 N 1 G I 11 | 17 488 N 1 A C 12 | 17 489 N 1 A C 13 | 17 490 N 1 A @ 14 | 17 491 N 1 T ; 15 | 17 492 N 1 G H 16 | 17 493 N 1 A H 17 | 17 494 N 1 A I 18 | 17 495 N 1 G L 19 | 17 496 N 1 A I 20 | 17 497 N 1 C H 21 | 17 498 N 1 A I 22 | 17 499 N 1 T I 23 | 17 500 N 1 A C 24 | 17 501 N 1 T F 25 | 17 502 N 1 G E 26 | 17 503 N 1 T K 27 | 17 504 N 1 C J 28 | 17 505 N 1 C < 29 | 17 506 N 1 A 9 30 | 17 507 N 1 C J 31 | 17 508 N 1 A I 32 | 17 509 N 1 C 9 33 | 17 510 N 1 A I 34 | 17 511 N 1 A < 35 | 17 512 N 1 A 3 36 | 17 513 N 1 A J 37 | 17 514 N 1 A 7 38 | 17 515 N 1 C I 39 | 17 516 N 1 C = 40 | 17 517 N 1 T E 41 | 17 518 N 1 G K 42 | 17 519 N 1 T B 43 | 17 520 N 1 T D 44 | 17 521 N 1 C F 45 | 17 522 N 1 A ? 46 | 17 523 N 1 T A 47 | 17 524 N 1 T 2 48 | 17 525 N 1 G F 49 | 17 526 N 1 C H 50 | 17 527 N 1 A I 51 | 17 528 N 1 G K 52 | 17 529 N 1 C 2 53 | 17 530 N 1 T B 54 | 17 531 N 1 T F 55 | 17 532 N 1 T F 56 | 17 533 N 1 C J 57 | 17 534 N 1 T J 58 | 17 535 N 1 A < 59 | 17 536 N 1 C F 60 | 17 537 N 1 C 2 61 | 17 538 N 1 A C 62 | 17 539 N 1 T H 63 | 17 540 N 1 C F 64 | 17 541 N 1 A I 65 | 17 542 N 1 C G 66 | 17 543 N 1 C J 67 | 17 544 N 1 A J 68 | 17 545 N 1 A C 69 | 17 546 N 1 A G 70 | 17 547 N 1 A J 71 | 17 548 N 1 A J 72 | 17 549 N 1 T F 73 | 17 550 N 1 T ; 74 | 17 551 N 1 G 8 75 | 17 552 N 1 C 3 76 | 17 553 N 1 A H 77 | 17 554 N 1 A C 78 | 17 555 N 1 A / 79 | 17 556 N 1 C K 80 | 17 557 N 1 A E 81 | 17 558 N 1 A ? 82 | 17 559 N 1 C I 83 | 17 560 N 1 C I 84 | 17 561 N 1 A 9 85 | 17 562 N 1 C I 86 | 17 563 N 1 A H 87 | 17 564 N 1 C 0 88 | 17 565 N 1 G > 89 | 17 566 N 1 C D 90 | 17 567 N 0 91 | 17 568 N 1 C J 92 | 17 569 N 1 T 5 93 | 17 570 N 1 T E 94 | 17 571 N 1 C @ 95 | 17 572 N 1 A F 96 | 17 573 N 1 A 6 97 | 17 574 N 1 C 9 98 | 17 575 N 1 T 7 99 | 17 576 N 1 G ? 100 | 17 577 N 1 G$ @ 101 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/31.out: -------------------------------------------------------------------------------- 1 | 17 478 N 1 ^]T B 2 | 17 479 N 1 A C 3 | 17 480 N 1 G G 4 | 17 481 N 1 G > 5 | 17 482 N 1 A E 6 | 17 483 N 1 G G 7 | 17 484 N 1 A 9 8 | 17 485 N 1 G G 9 | 17 486 N 1 A G 10 | 17 487 N 1 G I 11 | 17 488 N 1 A C 12 | 17 489 N 1 A C 13 | 17 490 N 1 A @ 14 | 17 491 N 1 T ; 15 | 17 492 N 1 G H 16 | 17 493 N 1 A H 17 | 17 494 N 1 A I 18 | 17 495 N 1 G L 19 | 17 496 N 1 A I 20 | 17 497 N 1 C H 21 | 17 498 N 1 A I 22 | 17 499 N 1 T I 23 | 17 500 N 1 A C 24 | 17 501 N 1 T F 25 | 17 502 N 1 G E 26 | 17 503 N 1 T K 27 | 17 504 N 1 C J 28 | 17 505 N 1 C < 29 | 17 506 N 1 A 9 30 | 17 507 N 1 C J 31 | 17 508 N 1 A I 32 | 17 509 N 1 C 9 33 | 17 510 N 1 A I 34 | 17 511 N 1 A < 35 | 17 512 N 1 A 3 36 | 17 513 N 1 A J 37 | 17 514 N 1 A 7 38 | 17 515 N 1 C I 39 | 17 516 N 1 C = 40 | 17 517 N 1 T E 41 | 17 518 N 1 G K 42 | 17 519 N 1 T B 43 | 17 520 N 1 T D 44 | 17 521 N 1 C F 45 | 17 522 N 1 A ? 46 | 17 523 N 1 T A 47 | 17 524 N 1 T 2 48 | 17 525 N 1 G F 49 | 17 526 N 1 C H 50 | 17 527 N 1 A I 51 | 17 528 N 1 G K 52 | 17 529 N 1 C 2 53 | 17 530 N 1 T B 54 | 17 531 N 1 T F 55 | 17 532 N 1 T F 56 | 17 533 N 1 C J 57 | 17 534 N 1 T J 58 | 17 535 N 1 A < 59 | 17 536 N 1 C F 60 | 17 537 N 1 C 2 61 | 17 538 N 1 A C 62 | 17 539 N 1 T H 63 | 17 540 N 1 C F 64 | 17 541 N 1 A I 65 | 17 542 N 1 C G 66 | 17 543 N 1 C J 67 | 17 544 N 1 A J 68 | 17 545 N 1 A C 69 | 17 546 N 1 A G 70 | 17 547 N 1 A J 71 | 17 548 N 1 A J 72 | 17 549 N 1 T F 73 | 17 550 N 1 T ; 74 | 17 551 N 1 G 8 75 | 17 552 N 1 C 3 76 | 17 553 N 1 A H 77 | 17 554 N 1 A C 78 | 17 555 N 1 A / 79 | 17 556 N 1 C K 80 | 17 557 N 1 A E 81 | 17 558 N 1 A ? 82 | 17 559 N 1 C I 83 | 17 560 N 1 C I 84 | 17 561 N 1 A 9 85 | 17 562 N 1 C I 86 | 17 563 N 1 A H 87 | 17 564 N 1 C 0 88 | 17 565 N 1 G > 89 | 17 566 N 1 C D 90 | 17 567 N 1 C ( 91 | 17 568 N 1 C J 92 | 17 569 N 1 T 5 93 | 17 570 N 1 T E 94 | 17 571 N 1 C @ 95 | 17 572 N 1 A F 96 | 17 573 N 1 A 6 97 | 17 574 N 1 C 9 98 | 17 575 N 1 T 7 99 | 17 576 N 1 G ? 100 | 17 577 N 1 G$ @ 101 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/32.out: -------------------------------------------------------------------------------- 1 | 17 478 N 1 ^]T B 2 | 17 479 N 1 A C 3 | 17 480 N 1 G G 4 | 17 481 N 1 G > 5 | 17 482 N 1 A E 6 | 17 483 N 1 G G 7 | 17 484 N 1 A 9 8 | 17 485 N 1 G G 9 | 17 486 N 1 A G 10 | 17 487 N 1 G I 11 | 17 488 N 1 A C 12 | 17 489 N 1 A C 13 | 17 490 N 1 A @ 14 | 17 491 N 1 T ; 15 | 17 492 N 1 G H 16 | 17 493 N 1 A H 17 | 17 494 N 1 A I 18 | 17 495 N 1 G L 19 | 17 496 N 1 A I 20 | 17 497 N 1 C H 21 | 17 498 N 1 A I 22 | 17 499 N 1 T I 23 | 17 500 N 1 A C 24 | 17 501 N 1 T F 25 | 17 502 N 1 G E 26 | 17 503 N 1 T K 27 | 17 504 N 1 C J 28 | 17 505 N 1 C < 29 | 17 506 N 1 A 9 30 | 17 507 N 1 C J 31 | 17 508 N 1 A I 32 | 17 509 N 1 C 9 33 | 17 510 N 1 A I 34 | 17 511 N 1 A < 35 | 17 512 N 1 A 3 36 | 17 513 N 1 A J 37 | 17 514 N 1 A 7 38 | 17 515 N 1 C I 39 | 17 516 N 1 C = 40 | 17 517 N 1 T E 41 | 17 518 N 1 G K 42 | 17 519 N 1 T B 43 | 17 520 N 1 T D 44 | 17 521 N 1 C F 45 | 17 522 N 1 A ? 46 | 17 523 N 1 T A 47 | 17 524 N 1 T 2 48 | 17 525 N 1 G F 49 | 17 526 N 1 C H 50 | 17 527 N 1 A I 51 | 17 528 N 1 G K 52 | 17 529 N 1 C 2 53 | 17 530 N 1 T B 54 | 17 531 N 1 T F 55 | 17 532 N 1 T F 56 | 17 533 N 1 C J 57 | 17 534 N 1 T J 58 | 17 535 N 1 A < 59 | 17 536 N 1 C F 60 | 17 537 N 1 C 2 61 | 17 538 N 1 A C 62 | 17 539 N 1 T H 63 | 17 540 N 1 C F 64 | 17 541 N 1 A I 65 | 17 542 N 1 C G 66 | 17 543 N 1 C J 67 | 17 544 N 1 A J 68 | 17 545 N 1 A C 69 | 17 546 N 1 A G 70 | 17 547 N 1 A J 71 | 17 548 N 1 A J 72 | 17 549 N 1 T F 73 | 17 550 N 1 T ; 74 | 17 551 N 1 G 8 75 | 17 552 N 1 C 3 76 | 17 553 N 1 A H 77 | 17 554 N 1 A C 78 | 17 555 N 1 A / 79 | 17 556 N 1 C K 80 | 17 557 N 1 A E 81 | 17 558 N 1 A ? 82 | 17 559 N 1 C I 83 | 17 560 N 1 C I 84 | 17 561 N 1 A 9 85 | 17 562 N 1 C I 86 | 17 563 N 1 A H 87 | 17 564 N 1 C 0 88 | 17 565 N 1 G > 89 | 17 566 N 1 C D 90 | 17 567 N 0 91 | 17 568 N 1 C J 92 | 17 569 N 1 T 5 93 | 17 570 N 1 T E 94 | 17 571 N 1 C @ 95 | 17 572 N 1 A F 96 | 17 573 N 1 A 6 97 | 17 574 N 1 C 9 98 | 17 575 N 1 T 7 99 | 17 576 N 1 G ? 100 | 17 577 N 1 G$ @ 101 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/33.out: -------------------------------------------------------------------------------- 1 | 17 1 A 1 ^].$ T 2 | 17 18 C 1 ^].$ B 3 | 17 23 A 1 ^]. T 4 | 17 24 T 1 . M 5 | 17 25 A 1 . N 6 | 17 26 G 1 . W 7 | 17 27 A 1 . K 8 | 17 28 T 1 . U 9 | 17 29 A 1 . ^ 10 | 17 30 A 1 . \ 11 | 17 31 T 1 . N 12 | 17 32 T 1 .$ R 13 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/34.out: -------------------------------------------------------------------------------- 1 | 17 1 A 0 2 | 17 18 C 0 3 | 17 23 A 1 ^]. D 4 | 17 24 T 1 . B 5 | 17 25 A 1 . D 6 | 17 26 G 1 . I 7 | 17 27 A 1 . G 8 | 17 28 T 1 . H 9 | 17 29 A 1 . G 10 | 17 30 A 1 . H 11 | 17 31 T 1 . E 12 | 17 32 T 1 .$ B 13 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/39.out: -------------------------------------------------------------------------------- 1 | 17 4000 N 15 ccCcccCCCCCcCcC DK5LJCIEICJAJLH 2 | 17 4001 N 15 ttTtttTTTTTtTtT EE:GGHIHLBJIKDJ 3 | 17 4002 N 15 ggGgggGGGGGgGgG CG3JJJHGFJIDKHG 4 | 17 4003 N 15 a$aAaaaAAAAAaAaA @D7IGHCDIAJCI7I 5 | 17 4004 N 14 tTtttTTTTTtTtT B2HCAIEHHHAI?F 6 | 17 4005 N 12 aaaaAAAAAaAA CHFGEEJEH@HG 7 | 17 4006 N 14 tTtttTTTTTtTtT C9FHGFGH>HJIKF 8 | 17 4007 N 14 tTtttTTTTTtTgT B2HFFEFG6EJH0G 9 | 17 4008 N 14 c$CcccCCCCCcCcC ?:HC;D6KJI?K/I 10 | 17 4009 N 13 CcccCCCCCcCcC 5IHI>AEGJLKLJ 11 | 17 4010 N 13 AaaaAAAAAaAaA >EEDHFI?IIIHJ 12 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/41.out: -------------------------------------------------------------------------------- 1 | CHROMOSOME_V 40 N 2 tG @~ 2 | CHROMOSOME_V 41 N 2 aC @~ 3 | CHROMOSOME_V 42 N 2 aC D~ 4 | CHROMOSOME_V 43 N 2 gT D~ 5 | CHROMOSOME_V 44 N 2 cA B~ 6 | CHROMOSOME_V 45 N 2 cA C~ 7 | CHROMOSOME_V 46 N 2 tG D~ 8 | CHROMOSOME_V 47 N 2 aC D~ 9 | CHROMOSOME_V 48 N 2 aC C~ 10 | CHROMOSOME_V 49 N 2 gT B~ 11 | CHROMOSOME_V 50 N 2 cA C~ 12 | CHROMOSOME_V 51 N 2 cA @~ 13 | CHROMOSOME_V 52 N 2 tG C~ 14 | CHROMOSOME_V 53 N 2 aC+10TTTTTTTTTT D~ 15 | CHROMOSOME_V 54 N 2 aC C~ 16 | CHROMOSOME_V 55 N 2 gT D~ 17 | CHROMOSOME_V 56 N 2 cA C~ 18 | CHROMOSOME_V 57 N 2 cA C~ 19 | CHROMOSOME_V 58 N 2 tG C~ 20 | CHROMOSOME_V 59 N 2 aC C~ 21 | CHROMOSOME_V 60 N 2 aC C~ 22 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/42.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/42.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/47.out: -------------------------------------------------------------------------------- 1 | 8500 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/5.out: -------------------------------------------------------------------------------- 1 | c1 1 A 2 ^!.^!. ** 2 | c1 2 A 4 ..^!.^!. **** 3 | c1 3 C 7 ....^!.^!.^!. ******* 4 | c1 4 C 7 .>..... *****'* 5 | c1 5 G 7 .>....+2NN. *****%* 6 | c1 6 C 7 .>..... *****%* 7 | c1 7 G 7 .>..... *****'* 8 | c1 8 G 7 .....$.$.$ ******* 9 | c1 9 T 4 ...$.$ **** 10 | c1 10 T 2 .$.$ ** 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/53.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=0.969697,1.0303 PL 89,0,40 22,0,43 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/54.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/55.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=0.833333,1.16667 PL 31,0,11 14,0,14 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/56.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/57.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=0.833333,1.16667 PL 29,0,10 13,0,13 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/58.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=0.969697,1.0303 PL 89,0,40 22,0,43 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/59.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/6.out: -------------------------------------------------------------------------------- 1 | c1 1 A 9 ^!.^!.^!.^!.^!.^!.^!.^!.^!. ~~~~~~~~~ 2 | c1 2 A 9 .........-3CCG ~~~~~~~~~ 3 | c1 3 C 9 ........* ~~~~~~~~~ 4 | c1 4 C 9 ........-1G* ~~~~~~~~~ 5 | c1 5 G 9 ....+6GTTAAC.+4TTAA.+3GTT.+3AAC*+2AG*+6TTAACT ~~~~~~~~~ 6 | c1 6 C 9 .......** ~~~~~~~~~ 7 | c1 7 G 9 ........* ~~~~~~~~~ 8 | c1 8 G 9 ........* ~~~~~~~~~ 9 | c1 9 T 9 ......... ~~~~~~~~~ 10 | c1 10 T 9 .$.$.$.$.$.$.$.$.$ ~~~~~~~~~ 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/60.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/60.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/61.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/62.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/62.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/63.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/64.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/64.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/65.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/66.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/66.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/67.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/68.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/68.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/69.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/69.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/7.out: -------------------------------------------------------------------------------- 1 | c1 1 A 12 ^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!* ~~~~~~~~~~~~ 2 | c1 2 A 12 ..........-3CCG.* ~~~~~~~~~~~~ 3 | c1 3 C 12 .........*.* ~~~~~~~~~~~~ 4 | c1 4 C 12 .........-1G*.-2GC* ~~~~~~~~~~~~ 5 | c1 5 G 13 .....+6GTTAAC.+4TTAA.+3GTT.+3AAC*+2AG*+6TTAACT**+2AN^!.+2TA$ ~~~~~~~~~~~~~ 6 | c1 6 C 12 ........**** ~~~~~~~~~~~! 7 | c1 7 G 12 .........*.* ~~~~~~~~~~~! 8 | c1 8 G 12 .........*.* ~~~~~~~~~~~! 9 | c1 9 T 12 ...........* ~~~~~~~~~~~! 10 | c1 10 T 12 .$.$.$.$.$.$.$.$.$.$.$*$ ~~~~~~~~~~~! 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/70.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/71.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/72.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/72.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/73.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/74.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/expected/74.out -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/75.out: -------------------------------------------------------------------------------- 1 | 17 547 . A AGCATCCTGCG 0 . INDEL;I16=2,0,1,2,404,81608,538,130834,120,7200,180,10800,38,722,63,1347;QS=1.01515,0.984848 PL 111,0,51 22,0,54 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/8.out: -------------------------------------------------------------------------------- 1 | c1 6 C 11 ^!.^!.^!.^!.^!.^!.^!.^!.^!*^!*^!* ~~~~~~~~~~~ 2 | c1 7 G 11 .........*. ~~~~~~~~~~~ 3 | c1 8 G 11 .........*. ~~~~~~~~~~~ 4 | c1 9 T 11 ........... ~~~~~~~~~~~ 5 | c1 10 T 11 .$.$.$.$.$.$.$.$.$.$.$ ~~~~~~~~~~~ 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/9.out: -------------------------------------------------------------------------------- 1 | xx 4 A 1 ^"n ! 2 | xx 5 A 1 n ! 3 | xx 6 A 1 n ! 4 | xx 7 A 1 n ! 5 | xx 8 A 1 n ! 6 | xx 9 A 1 n ! 7 | xx 10 A 1 n ! 8 | xx 11 T 1 n ! 9 | xx 12 T 1 n ! 10 | xx 13 T 1 n$ ! 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d1_1.out: -------------------------------------------------------------------------------- 1 | xx 6 1 2 | xx 7 1 3 | xx 8 1 4 | xx 13 1 5 | xx 14 1 6 | xx 15 1 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d1_12.out: -------------------------------------------------------------------------------- 1 | xx 6 1 0 2 | xx 7 1 1 3 | xx 8 1 1 4 | xx 9 0 1 5 | xx 11 0 1 6 | xx 12 0 1 7 | xx 13 1 1 8 | xx 14 1 0 9 | xx 15 1 0 10 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d1_2.out: -------------------------------------------------------------------------------- 1 | xx 7 1 2 | xx 8 1 3 | xx 9 1 4 | xx 11 1 5 | xx 12 1 6 | xx 13 1 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d2_12r.out: -------------------------------------------------------------------------------- 1 | xx 8 1 1 2 | xx 9 0 1 3 | xx 11 0 1 4 | xx 12 0 1 5 | xx 13 1 1 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d3_12.out: -------------------------------------------------------------------------------- 1 | xx 1 0 0 2 | xx 2 0 0 3 | xx 3 0 0 4 | xx 4 0 0 5 | xx 5 0 0 6 | xx 6 1 0 7 | xx 7 1 1 8 | xx 8 1 1 9 | xx 9 0 1 10 | xx 10 0 0 11 | xx 11 0 1 12 | xx 12 0 1 13 | xx 13 1 1 14 | xx 14 1 0 15 | xx 15 1 0 16 | xx 16 0 0 17 | xx 17 0 0 18 | xx 18 0 0 19 | xx 19 0 0 20 | xx 20 0 0 21 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d3_12r1a.out: -------------------------------------------------------------------------------- 1 | xx 5 0 0 2 | xx 6 1 0 3 | xx 7 1 1 4 | xx 8 1 1 5 | xx 9 0 1 6 | xx 10 0 0 7 | xx 11 0 1 8 | xx 12 0 1 9 | xx 13 1 1 10 | xx 14 1 0 11 | xx 15 1 0 12 | xx 16 0 0 13 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d3_12r2a.out: -------------------------------------------------------------------------------- 1 | xx 8 1 1 2 | xx 9 0 1 3 | xx 10 0 0 4 | xx 11 0 1 5 | xx 12 0 1 6 | xx 13 1 1 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d4_12.out: -------------------------------------------------------------------------------- 1 | xp 1 0 0 2 | xp 2 0 0 3 | xp 3 0 0 4 | xp 4 0 0 5 | xp 5 0 0 6 | xp 6 0 0 7 | xp 7 0 0 8 | xp 8 0 0 9 | xp 9 0 0 10 | xp 10 0 0 11 | xp 11 0 0 12 | xp 12 0 0 13 | xp 13 0 0 14 | xp 14 0 0 15 | xp 15 0 0 16 | xp 16 0 0 17 | xp 17 0 0 18 | xp 18 0 0 19 | xp 19 0 0 20 | xp 20 0 0 21 | xx 1 0 0 22 | xx 2 0 0 23 | xx 3 0 0 24 | xx 4 0 0 25 | xx 5 0 0 26 | xx 6 1 0 27 | xx 7 1 1 28 | xx 8 1 1 29 | xx 9 0 1 30 | xx 10 0 0 31 | xx 11 0 1 32 | xx 12 0 1 33 | xx 13 1 1 34 | xx 14 1 0 35 | xx 15 1 0 36 | xx 16 0 0 37 | xx 17 0 0 38 | xx 18 0 0 39 | xx 19 0 0 40 | xx 20 0 0 41 | xn 1 0 0 42 | xn 2 0 0 43 | xn 3 0 0 44 | xn 4 0 0 45 | xn 5 0 0 46 | xn 6 0 0 47 | xn 7 0 0 48 | xn 8 0 0 49 | xn 9 0 0 50 | xn 10 0 0 51 | xn 11 0 0 52 | xn 12 0 0 53 | xn 13 0 0 54 | xn 14 0 0 55 | xn 15 0 0 56 | xn 16 0 0 57 | xn 17 0 0 58 | xn 18 0 0 59 | xn 19 0 0 60 | xn 20 0 0 61 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d4_12b.out: -------------------------------------------------------------------------------- 1 | xp 11 0 0 2 | xp 12 0 0 3 | xp 13 0 0 4 | xp 14 0 0 5 | xp 15 0 0 6 | xx 5 0 0 7 | xx 6 1 0 8 | xx 7 1 1 9 | xx 8 1 1 10 | xx 9 0 1 11 | xx 10 0 0 12 | xx 11 0 1 13 | xx 12 0 1 14 | xx 13 1 1 15 | xx 14 1 0 16 | xx 15 1 0 17 | xx 16 0 0 18 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/expected/d4_12r.out: -------------------------------------------------------------------------------- 1 | xx 5 0 0 2 | xx 6 1 0 3 | xx 7 1 1 4 | xx 8 1 1 5 | xx 9 0 1 6 | xx 10 0 0 7 | xx 11 0 1 8 | xx 12 0 1 9 | xx 13 1 1 10 | xx 14 1 0 11 | xx 15 1 0 12 | xx 16 0 0 13 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/indels.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.0 SO:coordinate 2 | @SQ SN:17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human 3 | @RG ID:A SM:A PL:ILLUMINA 4 | @RG ID:B SM:B PL:LS454 5 | A.in1 99 17 478 60 70M10I30M = 528 150 TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAGCATCCTGCGATTGCAAACAACCACACGCCCTTCAACTGG BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:A 6 | A.in1 147 17 528 60 20M10I80M = 470 -150 GCTTTCTACCATCACCAAAAGCATCCTGCGATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCAC BCG>EG9GGICC@;HHILIHAAAAAAAAAAIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:A 7 | A.out1 99 17 528 60 100M = 470 -150 GCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCAC BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:A 8 | B.in1 147 17 528 60 20M10I80M = 470 -150 GCTTTCTACCATCACCAAAAGCATGGTGCGATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCAC BCG>EG9GGICC@;HHILIHAAAAAAAAAAIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:B 9 | B.out1 99 17 528 60 100M = 470 -150 GCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCAC BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:B 10 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae: -------------------------------------------------------------------------------- 1 | CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGAAGAGACCAAACCGAAAAATCAATTTTTTAAACGAAAAATCAATGTTTTA -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d: -------------------------------------------------------------------------------- 1 | CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAAGCGCGAAATCCTATGAAATTTCAAGGATTTATAACTTTTTGAGTCCGAAAAGAGTCGGAAATCAGAT -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc: -------------------------------------------------------------------------------- 1 | GAATTCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCATAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCATAAGCCTAAGCCT -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1: -------------------------------------------------------------------------------- 1 | GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGC -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e: -------------------------------------------------------------------------------- 1 | CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAATAGTGACTCTGGCAGTTCTCTAAAA -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/mpileup-E.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/mpileup-E.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/mpileup.1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/mpileup.1.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/mpileup.1.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/mpileup.1.bam.bai -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/mpileup.2.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/mpileup.2.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/mpileup.3.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/mpileup.3.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/mpileup.ref.fa.fai: -------------------------------------------------------------------------------- 1 | 17 4200 14 60 61 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/overlap50.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.0 SO:coordinate 2 | @SQ SN:17 LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz AS:NCBI37 SP:Human 3 | @RG ID:ERR162872 LB:3815246 SM:HG00100 PI:349 CN:SC PL:ILLUMINA DS:SRP001294 4 | foo2 99 17 478 60 100M = 528 150 TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGG BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:ERR162872 5 | foo2 147 17 528 60 100M = 470 -150 GCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCAC BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJD(J5E@F697?@ RG:Z:ERR162872 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/overlapIllumina.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/overlapIllumina.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/regions: -------------------------------------------------------------------------------- 1 | browser position CHROMOSOME_I:1-100 2 | browser hide all 3 | CHROMOSOME_I 50 50 4 | CHROMOSOME_II 49 60 5 | CHROMOSOME_II 59 70 overlap-test 6 | CHROMOSOME_III 39 40 7 | CHROMOSOME_III 50 8 | CHROMOSOME_V 49 60 bed_example3~3~ 99 + 11 12 0 2 567,488, 0,3512 9 | CHROMOSOME_V 19 80 10 | 11 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx#depth1.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:xp LN:20 AS:? SP:? UR:? M5:bbf4de6d8497a119dda6e074521643dc 3 | @SQ SN:xx LN:20 AS:? SP:? UR:? M5:bbf4de6d8497a119dda6e074521643dc 4 | @SQ SN:xn LN:20 AS:? SP:? UR:? M5:bbf4de6d8497a119dda6e074521643dc 5 | a1 16 xx 6 1 3M * 0 0 * * 6 | b1 16 xx 13 1 3M * 0 0 * * 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx#depth2.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @SQ SN:xp LN:20 AS:? SP:? UR:? M5:bbf4de6d8497a119dda6e074521643dc 3 | @SQ SN:xx LN:20 AS:? SP:? UR:? M5:bbf4de6d8497a119dda6e074521643dc 4 | @SQ SN:xn LN:20 AS:? SP:? UR:? M5:bbf4de6d8497a119dda6e074521643dc 5 | a1 16 xx 7 1 3M * 0 0 * * 6 | b1 16 xx 11 1 3M * 0 0 * * 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx#minimal.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/xx#minimal.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx#triplet.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/mpileup/xx#triplet.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx.bed: -------------------------------------------------------------------------------- 1 | xp 10 15 2 | xx 4 16 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx.bed2: -------------------------------------------------------------------------------- 1 | xx 7 13 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx.fa: -------------------------------------------------------------------------------- 1 | >xx 2 | AAAAAAAAAATTTTTTTTTTCCCCC 3 | >yy 4 | AAAAAAAAAATTTTTTTTTT 5 | 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/mpileup/xx.fa.fai: -------------------------------------------------------------------------------- 1 | xx 25 4 25 26 2 | yy 20 34 20 21 3 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/quickcheck/1.quickcheck.badeof.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/quickcheck/1.quickcheck.badeof.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/quickcheck/2.quickcheck.badheader.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/quickcheck/2.quickcheck.badheader.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/quickcheck/3.quickcheck.ok.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/quickcheck/3.quickcheck.ok.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/quickcheck/4.quickcheck.ok.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/quickcheck/4.quickcheck.ok.bam -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/quickcheck/5.quickcheck.truncated.cram: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/quickcheck/5.quickcheck.truncated.cram -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/quickcheck/all.expected: -------------------------------------------------------------------------------- 1 | 1.quickcheck.badeof.bam 2 | 2.quickcheck.badheader.bam 3 | 5.quickcheck.truncated.cram 4 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/reheader/1_view1.sam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/reheader/1_view1.sam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/reheader/2_view1.sam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/reheader/2_view1.sam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/reheader/3_view1.sam.expected.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/test/reheader/3_view1.sam.expected.err -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/reheader/hdr.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 SO:coordinate 2 | @RG ID:grp1 DS:Group_1 LB:Library_1 SM:Sample 3 | @RG ID:grp2 DS:Group_2 LB:Library_2 SM:Sample 4 | @RG ID:grp3 DS:Group_3 LB:Library_3 SM:Sample 5 | @PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 6 | @CO The MIT License 7 | @CO 8 | @CO Copyright (c) 2014 Genome Research Ltd. 9 | @CO 10 | @CO Permission is hereby granted, free of charge, to any person obtaining a copy 11 | @CO of this software and associated documentation files (the "Software"), to deal 12 | @CO in the Software without restriction, including without limitation the rights 13 | @CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 14 | @CO copies of the Software, and to permit persons to whom the Software is 15 | @CO furnished to do so, subject to the following conditions: 16 | @CO 17 | @CO The above copyright notice and this permission notice shall be included in 18 | @CO all copies or substantial portions of the Software. 19 | @CO 20 | @CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 21 | @CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 22 | @CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 23 | @CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 24 | @CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 25 | @CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 26 | @CO THE SOFTWARE. 27 | @SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 28 | @SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 29 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/10_map_cigar.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | @RG ID:s1_b_1 LB:1 SM:s1 5 | r1 99 alpha 1 40 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:s1_a_1 NM:i:0 6 | r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 7 | r1 99 alpha 1 40 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:s1_b_1 NM:i:0 8 | r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_b_1 NM:i:0 9 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/1_map_cigar.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:s1_a_1 NM:i:0 5 | r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/2_equal_cigar_full_seq.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 35= = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:s1_a_1 NM:i:0 5 | r1 147 alpha 66 40 35= = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/3_map_cigar_equal_seq.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 35M = 66 100 =================================== * RG:Z:s1_a_1 NM:i:0 5 | r1 147 alpha 66 40 35M = 1 -100 =================================== * RG:Z:s1_a_1 NM:i:0 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/4_X_cigar_full_seq.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 34M1X = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGC * RG:Z:s1_a_1 NM:i:0 5 | r1 147 alpha 66 40 35= = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/5_insert_cigar.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 1M1I33M = 66 100 TGGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAG * RG:Z:s1_a_1 NM:i:0 5 | r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 6 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/7_supp.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 1M1I30M3S = 66 100 TGGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAG * RG:Z:s1_a_1 NM:i:0 5 | r1 2147 alpha 1 40 30H1M1I1M = 66 100 GAG * RG:Z:s1_a_1 NM:i:0 6 | r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/8_secondary.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.4 2 | @SQ SN:alpha LN:100 3 | @RG ID:s1_a_1 LB:1 SM:s1 4 | r1 99 alpha 1 40 1M1I33M = 66 100 TGGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAG * RG:Z:s1_a_1 NM:i:0 5 | r1 355 alpha 1 80 2M1I32M = 66 100 TGGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAG * RG:Z:s1_a_1 NM:i:0 6 | r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 7 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/test.fa: -------------------------------------------------------------------------------- 1 | >alpha 2 | tggggtgtcatagtaatccggttgggagtccgaggctaagaatattcatttagaggtcgg 3 | catattatccagaactttgcagccatatctccaagacatg 4 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/stat/test.fa.fai: -------------------------------------------------------------------------------- 1 | alpha 100 7 60 61 2 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/test.c: -------------------------------------------------------------------------------- 1 | /* test/test.c -- test harness utility routines. 2 | 3 | Copyright (C) 2014 Genome Research Ltd. 4 | 5 | Author: Martin O. Pollard 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 26 | 27 | #include 28 | #include 29 | #include 30 | #include 31 | #include 32 | 33 | #include "test.h" 34 | 35 | void xfreopen(const char *path, const char *mode, FILE *stream) 36 | { 37 | if (freopen(path, mode, stream) == NULL) { 38 | fprintf(stderr, __FILE__": error reopening %s: %s\n", 39 | path, strerror(errno)); 40 | exit(2); 41 | } 42 | } 43 | 44 | void dump_hdr(const bam_hdr_t* hdr) 45 | { 46 | printf("n_targets: %d\n", hdr->n_targets); 47 | printf("ignore_sam_err: %d\n", hdr->ignore_sam_err); 48 | printf("l_text: %u\n", hdr->l_text); 49 | printf("idx\ttarget_len\ttarget_name:\n"); 50 | int32_t target; 51 | for (target = 0; target < hdr->n_targets; ++target) { 52 | printf("%d\t%u\t\"%s\"\n", target, hdr->target_len[target], hdr->target_name[target]); 53 | } 54 | printf("text: \"%s\"\n", hdr->text); 55 | } 56 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/test/test.h: -------------------------------------------------------------------------------- 1 | /* test/test.h -- test harness utility routines. 2 | 3 | Copyright (C) 2014 Genome Research Ltd. 4 | 5 | Author: Martin O. Pollard 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 TEST_H 26 | #define TEST_H 27 | 28 | #include 29 | #include 30 | 31 | void xfreopen(const char *path, const char *mode, FILE *stream); 32 | 33 | void dump_hdr(const bam_hdr_t* hdr); 34 | 35 | #endif 36 | -------------------------------------------------------------------------------- /src/samtools-1.3.1/win32/libcurses.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/win32/libcurses.a -------------------------------------------------------------------------------- /src/samtools-1.3.1/win32/libz.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/speedseq/4e60002cb7d6af3afd9fa3236ddfef8a897f29fe/src/samtools-1.3.1/win32/libz.a --------------------------------------------------------------------------------