├── .dictionary ├── .gitattributes ├── .github ├── CONTRIBUTING.md └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .landscape.yaml ├── .mailmap ├── .travis.yml ├── .ycm_extra_conf.py ├── CHANGELOG.md ├── CITATION ├── CODE_OF_CONDUCT.rst ├── Doxyfile.in ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── author-skips.txt ├── authors.csv ├── ci_scripts └── install.sh ├── data ├── 100k-filtered.fa ├── 100k-surrendered.fa ├── 25k-casava1_8.fq.bz2 ├── 25k.fq.gz ├── inconsistent.fa ├── sequential-shuffled.fa ├── sequential.fa ├── stamps-genomes.fa └── stamps-reads.fa.gz ├── doc ├── LICENSE.rst ├── Makefile ├── _static │ ├── labibi.css │ └── labibi.js ├── _templates │ └── page.html ├── citations.rst ├── conf.py ├── contributors.rst ├── dev │ ├── CODE_OF_CONDUCT.rst │ ├── a-quick-guide-to-testing.rst │ ├── binary-file-formats.rst │ ├── codebase-guide.rst │ ├── development.rst │ ├── for-khmer-developers.rst │ ├── getting-started.rst │ ├── guidelines-continued-dev.rst │ ├── hackathon.rst │ ├── index.rst │ ├── python-api.rst │ ├── release.rst │ └── scripts-and-sandbox.rst ├── index.rst ├── introduction.rst ├── libstdc++.tag ├── release-notes │ ├── index.rst │ ├── release-1.0.1.md │ ├── release-1.0.1.rst │ ├── release-1.0.md │ ├── release-1.0.rst │ ├── release-1.1.md │ ├── release-1.1.rst │ ├── release-1.2.md │ ├── release-1.2.rst │ ├── release-1.3.md │ ├── release-1.3.rst │ ├── release-1.4.md │ ├── release-1.4.rst │ ├── release-2.0.md │ ├── release-2.0.rst │ ├── release-2.1.md │ └── release-2.1.rst ├── requirements.txt ├── roadmap.rst ├── run-corn-50m.sh └── user │ ├── api-examples.rst │ ├── artifact-removal.graffle │ ├── artifact-removal.png │ ├── biblio.rst │ ├── blog-posts.rst │ ├── choosing-table-sizes.rst │ ├── examples.rst │ ├── galaxy.rst │ ├── getting-help.rst │ ├── guide.rst │ ├── index.rst │ ├── install.rst │ ├── known-issues.rst │ ├── partitioning-big-data.rst │ ├── partitioning-workflow.graffle │ ├── partitioning-workflow.png │ └── scripts.rst ├── docker └── Dockerfile ├── examples ├── c++-api │ ├── .gitignore │ ├── Makefile │ ├── bloom.cc │ ├── consume.cc │ ├── exact-counting.cc │ └── reads.fastq ├── python-api │ ├── bloom.py │ ├── consume.py │ ├── exact-counting.py │ └── mask.py ├── python-nullomers │ └── find-nullomers.py ├── stamps k-mer distributions.ipynb └── stamps │ └── do.sh ├── ez_setup.py ├── include ├── khmer │ ├── .gitignore │ ├── _cpy_khmer.hh │ ├── _cpy_readparsers.hh │ └── _cpy_utils.hh └── oxli │ ├── .gitignore │ ├── alphabets.hh │ ├── assembler.hh │ ├── hashgraph.hh │ ├── hashtable.hh │ ├── hllcounter.hh │ ├── kmer_filters.hh │ ├── kmer_hash.hh │ ├── labelhash.hh │ ├── magic │ ├── oxli.hh │ ├── oxli_exception.hh │ ├── read_aligner.hh │ ├── read_parsers.hh │ ├── storage.hh │ ├── subset.hh │ └── traversal.hh ├── khmer ├── __init__.py ├── _oxli │ ├── __init__.py │ ├── assembly.cpp │ ├── assembly.pxd │ ├── assembly.pyx │ ├── graphs.cpp │ ├── graphs.pxd │ ├── graphs.pyx │ ├── hashing.cpp │ ├── hashing.pxd │ ├── hashing.pyx │ ├── hashset.cpp │ ├── hashset.pxd │ ├── hashset.pyx │ ├── hllcounter.cpp │ ├── hllcounter.pxd │ ├── hllcounter.pyx │ ├── labeling.cpp │ ├── labeling.pxd │ ├── labeling.pyx │ ├── legacy_partitioning.cpp │ ├── legacy_partitioning.pxd │ ├── legacy_partitioning.pyx │ ├── oxli_exception_convert.cc │ ├── oxli_exception_convert.hh │ ├── oxli_types.pxd │ ├── parsing.cpp │ ├── parsing.pxd │ ├── parsing.pyx │ ├── readaligner.cpp │ ├── readaligner.pxd │ ├── readaligner.pyx │ ├── traversal.cpp │ ├── traversal.pxd │ ├── traversal.pyx │ ├── utils.cpp │ ├── utils.pxd │ └── utils.pyx ├── _version.py ├── kfile.py ├── khmer_args.py ├── khmer_logger.py ├── thread_utils.py ├── trimming.py └── utils.py ├── legacy ├── ChangeLog └── jenkins-build.sh ├── oxli ├── __init__.py ├── build_graph.py ├── functions.py └── partition.py ├── papers └── paper-v2.1.md ├── pylintrc ├── pytest.ini ├── sandbox ├── Makefile.read_aligner_training ├── README.rst ├── assemble-and-track.py ├── assemble-on-the-go.py ├── assembly-diff-2.py ├── assembly-diff.py ├── assemstats3.py ├── bloom-count.py ├── build-sparse-graph.py ├── calc-best-assembly.py ├── calc-error-profile.py ├── calc-median-distribution.py ├── collect-reads.py ├── collect-variants.py ├── correct-reads.py ├── count-kmers-single.py ├── count-kmers.py ├── error-correct-pass2.py ├── estimate_optimal_hash.py ├── extract-compact-dbg.py ├── extract-single-partition.py ├── extract-unassembled-reads-2.py ├── extract-unassembled-reads.py ├── filter-below-abund.py ├── filter-median-and-pct.py ├── filter-median.py ├── graph-size.py ├── link-compact-dbg.py ├── make-coverage.py ├── memusg ├── multi-rename.py ├── normalize-by-median-pct.py ├── optimal_args_hashbits.py ├── print-stoptags.py ├── print-tagset.py ├── readaligner_pairhmm_train.py ├── reassemble-contigs.py ├── renumber-partitions.py ├── saturate-by-median.py ├── shuffle-reverse-rotary.py ├── slice-reads-by-coverage.py ├── split-fasta.py ├── split-sequences-by-length.py ├── stoptag-abundance-hist.py ├── stoptags-by-position.py ├── streaming-assembly-simple.py ├── strip-partition.py ├── subset-report.py ├── sweep-files.py ├── sweep-out-reads-with-contigs.py ├── sweep-reads.py ├── sweep-reads2.py ├── sweep-reads3.py └── write-trimmomatic.py ├── scripts ├── .gitignore ├── abundance-dist-single.py ├── abundance-dist.py ├── annotate-partitions.py ├── count-median.py ├── do-partition.py ├── extract-long-sequences.py ├── extract-paired-reads.py ├── extract-partitions.py ├── fastq-to-fasta.py ├── filter-abund-single.py ├── filter-abund.py ├── filter-stoptags.py ├── find-knots.py ├── interleave-reads.py ├── load-graph.py ├── load-into-counting.py ├── make-initial-stoptags.py ├── merge-partitions.py ├── normalize-by-median.py ├── oxli ├── partition-graph.py ├── readstats.py ├── sample-reads-randomly.py ├── split-paired-reads.py ├── trim-low-abund.py └── unique-kmers.py ├── setup.cfg ├── setup.py ├── sort-authors-list.py ├── src ├── khmer │ ├── .gitignore │ ├── _cpy_hashtable.cc │ ├── _cpy_khmer.cc │ ├── _cpy_readparsers.cc │ └── _cpy_utils.cc └── oxli │ ├── .check_openmp.cc │ ├── .gitignore │ ├── Makefile │ ├── alphabets.cc │ ├── assembler.cc │ ├── hashgraph.cc │ ├── hashtable.cc │ ├── hllcounter.cc │ ├── kmer_filters.cc │ ├── kmer_hash.cc │ ├── labelhash.cc │ ├── oxli.pc.in │ ├── read_aligner.cc │ ├── read_parsers.cc │ ├── storage.cc │ ├── subset.cc │ ├── test-Colors.cc │ ├── test-compile.cc │ └── traversal.cc ├── tests ├── .gitignore ├── __init__.py ├── graph_features.py ├── khmer_tst_utils.py ├── table_fixtures.py ├── test-data │ ├── 100-reads.fq.bz2 │ ├── 100-reads.fq.gz │ ├── 100-reads.fq.truncated.bz2 │ ├── 100-reads.fq.truncated.gz │ ├── README.rst │ ├── all-A.fa │ ├── badversion-k12.ct │ ├── badversion-k12.ht │ ├── badversion-k32.stoptags │ ├── badversion-k32.tagset │ ├── banding-reads.fq │ ├── biglump-random-20-a.fa │ ├── bogus.fa │ ├── branched-genome.fa │ ├── casava_18-pe.fq │ ├── combine_parts_1.fa │ ├── dn-test-all-paired-all-keep.fa │ ├── dn-test-none-paired.fa │ ├── dn-test-some-paired-all-keep.fa │ ├── empty-file │ ├── empty-file.bz2 │ ├── empty-file.gz │ ├── fakelump.fa │ ├── fakelump.fa.stoptags.txt │ ├── filter-test-A.fa │ ├── filter-test-B.fa │ ├── goodversion-k12.ht │ ├── goodversion-k12.ht.gz │ ├── goodversion-k32.stoptags │ ├── goodversion-k32.tagset │ ├── multi-output.fa │ ├── normC20k20.ct │ ├── old-style-format-w-comments.fq │ ├── paired-broken.fq.1 │ ├── paired-broken.fq.2 │ ├── paired-broken.fq.badleft │ ├── paired-broken.fq.badright │ ├── paired-broken.fq.paired_bad │ ├── paired-broken2.fq.1 │ ├── paired-broken2.fq.2 │ ├── paired-broken3.fq.1 │ ├── paired-broken3.fq.2 │ ├── paired-broken4.fq.1 │ ├── paired-broken4.fq.2 │ ├── paired-mixed-2.fq │ ├── paired-mixed-broken.fq │ ├── paired-mixed-witherror.fa.pe │ ├── paired-mixed.fa │ ├── paired-mixed.fa.pe │ ├── paired-mixed.fa.se │ ├── paired-mixed.fq │ ├── paired-mixed.fq.pe │ ├── paired-mixed.fq.se │ ├── paired-slash1.fq │ ├── paired-slash1.fq.1 │ ├── paired-slash1.fq.2 │ ├── paired.fa │ ├── paired.fa.1 │ ├── paired.fa.2 │ ├── paired.fq │ ├── paired.fq.1 │ ├── paired.fq.2 │ ├── paired.malformat.fq │ ├── paired.malformat.fq.2 │ ├── paired_one.base.dif.fa │ ├── random-20-X2.fa │ ├── random-20-a.even.fa │ ├── random-20-a.fa │ ├── random-20-a.fa.bz2 │ ├── random-20-a.fa.gz │ ├── random-20-a.fa.part │ ├── random-20-a.fq │ ├── random-20-a.fq.bz2 │ ├── random-20-a.fq.gz │ ├── random-20-a.odd.fa │ ├── random-20-b.fa │ ├── random-31-c.fa │ ├── readaligner-default.json │ ├── readaligner-k12.json │ ├── real-partition-small.fa │ ├── real-partition-tiny.fa │ ├── seq-a.fa │ ├── seq-b.fa │ ├── simple-genome-reads.fa │ ├── simple-genome.fa │ ├── single-read.fa │ ├── single-read.fq │ ├── test-abund-read-2.fa │ ├── test-abund-read-2.fa.bz2 │ ├── test-abund-read-2.fa.gz │ ├── test-abund-read-2.fq │ ├── test-abund-read-2.paired.fq │ ├── test-abund-read-2.paired2.fq │ ├── test-abund-read-3.fa │ ├── test-abund-read-impaired.fa │ ├── test-abund-read-paired.fa │ ├── test-abund-read-paired.fq │ ├── test-abund-read.fa │ ├── test-empty.fa │ ├── test-empty.fa.bz2 │ ├── test-error-reads.fq │ ├── test-fastq-n-reads.fq │ ├── test-fastq-reads.fa │ ├── test-fastq-reads.fq │ ├── test-filter-abund-Ns.fq │ ├── test-graph.fa │ ├── test-graph2.fa │ ├── test-graph5.fa │ ├── test-labels.fa │ ├── test-large.fa │ ├── test-multi.fa │ ├── test-output-partitions.fa │ ├── test-overlap1.fa │ ├── test-overlap2.fa │ ├── test-reads.fa │ ├── test-reads.fq.bz2 │ ├── test-reads.fq.gz │ ├── test-short.fa │ ├── test-sweep-contigs.fp │ ├── test-sweep-reads.fa │ ├── test-sweep-reads.fq │ ├── test-transcript.fa │ ├── truncated.fq │ ├── unclean-reads.fastq │ └── valid-read-testing.fq ├── test_assembly.py ├── test_banding.py ├── test_countgraph.py ├── test_counting_single.py ├── test_counttable.py ├── test_cpython_hierarchy.py ├── test_cython_parsing.py ├── test_filter_abund.py ├── test_functions.py ├── test_graph.py ├── test_hashset.py ├── test_hll.py ├── test_labelhash.py ├── test_lump.py ├── test_memory.py ├── test_nibblestorage.py ├── test_nodegraph.py ├── test_normalize_by_median.py ├── test_oxli_functions.py ├── test_qfstorage.py ├── test_read_aligner.py ├── test_read_handling.py ├── test_read_parsers.py ├── test_sandbox_scripts.py ├── test_script_arguments.py ├── test_script_output.py ├── test_scripts.py ├── test_sequence_validation.py ├── test_streaming_io.py ├── test_subset_graph.py ├── test_tabletype.py ├── test_threaded_sequence_processor.py └── test_version.py ├── third-party ├── .gitignore ├── bzip2 │ ├── .gitignore │ ├── CHANGES │ ├── LICENSE │ ├── Makefile │ ├── Makefile-libbz2_so │ ├── README │ ├── README.COMPILATION.PROBLEMS │ ├── README.XML.STUFF │ ├── blocksort.c │ ├── bz-common.xsl │ ├── bz-fo.xsl │ ├── bz-html.xsl │ ├── bzdiff │ ├── bzdiff.1 │ ├── bzgrep │ ├── bzgrep.1 │ ├── bzip.css │ ├── bzip2.1 │ ├── bzip2.1.preformatted │ ├── bzip2.c │ ├── bzip2.txt │ ├── bzip2recover.c │ ├── bzlib.c │ ├── bzlib.h │ ├── bzlib_private.h │ ├── bzmore │ ├── bzmore.1 │ ├── compress.c │ ├── crctable.c │ ├── decompress.c │ ├── dlltest.c │ ├── dlltest.dsp │ ├── entities.xml │ ├── format.pl │ ├── huffman.c │ ├── libbz2.def │ ├── libbz2.dsp │ ├── makefile.msc │ ├── manual.html │ ├── manual.pdf │ ├── manual.ps │ ├── manual.xml │ ├── mk251.c │ ├── randtable.c │ ├── sample1.bz2 │ ├── sample1.ref │ ├── sample2.bz2 │ ├── sample2.ref │ ├── sample3.bz2 │ ├── sample3.ref │ ├── spewG.c │ ├── unzcrash.c │ ├── words0 │ ├── words1 │ ├── words2 │ ├── words3 │ └── xmlproc.sh ├── cqf │ ├── LICENSE │ ├── Makefile │ ├── README.md │ ├── gqf.c │ └── gqf.h ├── rollinghash │ ├── README.md │ ├── characterhash.h │ └── cyclichash.h ├── seqan │ ├── ChangeLog │ ├── LICENSE │ ├── README │ └── core │ │ └── include │ │ └── seqan │ │ ├── align.h │ │ ├── align │ │ ├── INFO │ │ ├── align_base.h │ │ ├── align_cols.h │ │ ├── align_config.h │ │ ├── align_iterator_base.h │ │ ├── align_metafunctions.h │ │ ├── align_traceback.h │ │ ├── alignment_algorithm_tags.h │ │ ├── alignment_operations.h │ │ ├── dp_algorithm_impl.h │ │ ├── dp_band.h │ │ ├── dp_cell.h │ │ ├── dp_cell_affine.h │ │ ├── dp_cell_linear.h │ │ ├── dp_formula.h │ │ ├── dp_formula_affine.h │ │ ├── dp_formula_linear.h │ │ ├── dp_matrix.h │ │ ├── dp_matrix_navigator.h │ │ ├── dp_matrix_navigator_score_matrix.h │ │ ├── dp_matrix_navigator_score_matrix_sparse.h │ │ ├── dp_matrix_navigator_trace_matrix.h │ │ ├── dp_matrix_sparse.h │ │ ├── dp_meta_info.h │ │ ├── dp_profile.h │ │ ├── dp_scout.h │ │ ├── dp_setup.h │ │ ├── dp_trace_segment.h │ │ ├── dp_traceback_adaptor.h │ │ ├── dp_traceback_impl.h │ │ ├── gap_anchor.h │ │ ├── gapped_value_type.h │ │ ├── gaps_anchor.h │ │ ├── gaps_array.h │ │ ├── gaps_base.h │ │ ├── gaps_iterator_anchor.h │ │ ├── gaps_iterator_array.h │ │ ├── gaps_iterator_base.h │ │ ├── global_alignment_banded.h │ │ ├── global_alignment_hirschberg_impl.h │ │ ├── global_alignment_myers_hirschberg_impl.h │ │ ├── global_alignment_myers_impl.h │ │ ├── global_alignment_specialized.h │ │ ├── global_alignment_unbanded.h │ │ ├── local_alignment_banded.h │ │ ├── local_alignment_banded_waterman_eggert_impl.h │ │ ├── local_alignment_enumeration.h │ │ ├── local_alignment_enumeration_banded.h │ │ ├── local_alignment_enumeration_unbanded.h │ │ ├── local_alignment_unbanded.h │ │ ├── local_alignment_waterman_eggert_impl.h │ │ └── matrix_base.h │ │ ├── bam_io.h │ │ ├── bam_io │ │ ├── INFO │ │ ├── bam_alignment_record.h │ │ ├── bam_alignment_record_util.h │ │ ├── bam_header_record.h │ │ ├── bam_index_bai.h │ │ ├── bam_index_base.h │ │ ├── bam_io_context.h │ │ ├── bam_reader.h │ │ ├── bam_sam_conversion.h │ │ ├── bam_stream.h │ │ ├── bam_tags_dict.h │ │ ├── bam_writer.h │ │ ├── cigar.h │ │ ├── read_bam.h │ │ ├── read_sam.h │ │ ├── sam_reader.h │ │ ├── sam_writer.h │ │ ├── write_bam.h │ │ ├── write_sam.h │ │ ├── xam_reader.h │ │ └── xam_writer.h │ │ ├── basic.h │ │ ├── basic │ │ ├── INFO │ │ ├── aggregate_concept.h │ │ ├── allocator_chunkpool.h │ │ ├── allocator_interface.h │ │ ├── allocator_multipool.h │ │ ├── allocator_simple.h │ │ ├── allocator_singlepool.h │ │ ├── allocator_to_std.h │ │ ├── alphabet_adapt_builtins.h │ │ ├── alphabet_bio.h │ │ ├── alphabet_concept.h │ │ ├── alphabet_math.h │ │ ├── alphabet_profile.h │ │ ├── alphabet_qualities.h │ │ ├── alphabet_residue.h │ │ ├── alphabet_residue_tabs.h │ │ ├── alphabet_simple_type.h │ │ ├── alphabet_storage.h │ │ ├── array_construct_destruct.h │ │ ├── basic_aggregate.h │ │ ├── basic_allocator.h │ │ ├── basic_alphabet.h │ │ ├── basic_concept.h │ │ ├── basic_container.h │ │ ├── basic_debug.h │ │ ├── basic_fundamental.h │ │ ├── basic_iterator.h │ │ ├── basic_math.h │ │ ├── basic_metaprogramming.h │ │ ├── basic_parallelism.h │ │ ├── basic_proxy.h │ │ ├── basic_smart_pointer.h │ │ ├── basic_tangle.h │ │ ├── basic_type.h │ │ ├── boost_preprocessor_subset.h │ │ ├── builtin_functions.h │ │ ├── concept_checking.h │ │ ├── container_concept.h │ │ ├── debug_helper.h │ │ ├── debug_test_system.h │ │ ├── fundamental_comparison.h │ │ ├── fundamental_concepts.h │ │ ├── fundamental_conversion.h │ │ ├── fundamental_metafunctions.h │ │ ├── fundamental_tags.h │ │ ├── fundamental_transport.h │ │ ├── holder_base.h │ │ ├── holder_simple.h │ │ ├── holder_tristate.h │ │ ├── hosted_type_interface.h │ │ ├── iterator_adapt_pointer.h │ │ ├── iterator_adapt_std.h │ │ ├── iterator_adaptor.h │ │ ├── iterator_base.h │ │ ├── iterator_concept.h │ │ ├── iterator_interface.h │ │ ├── iterator_position.h │ │ ├── macro_deprecated.h │ │ ├── math_functions.h │ │ ├── math_log_space_value.h │ │ ├── metaprogramming_control.h │ │ ├── metaprogramming_enable_if.h │ │ ├── metaprogramming_logic.h │ │ ├── metaprogramming_math.h │ │ ├── metaprogramming_type.h │ │ ├── pair_base.h │ │ ├── pair_bit_compressed.h │ │ ├── pair_packed.h │ │ ├── profiling.h │ │ ├── proxy_base.h │ │ ├── proxy_iterator.h │ │ ├── test_system.h │ │ ├── triple_base.h │ │ ├── triple_packed.h │ │ ├── tuple_base.h │ │ ├── tuple_bit_compressed.h │ │ └── volatile_ptr.h │ │ ├── file.h │ │ ├── file │ │ ├── INFO │ │ ├── chunk_collector.h │ │ ├── cstream.h │ │ ├── file_base.h │ │ ├── file_cstyle.h │ │ ├── file_filereader.h │ │ ├── file_filereaderiterator.h │ │ ├── file_format.h │ │ ├── file_format_cgviz.h │ │ ├── file_format_embl.h │ │ ├── file_format_fasta.h │ │ ├── file_format_fasta_align.h │ │ ├── file_format_genbank.h │ │ ├── file_format_guess.h │ │ ├── file_format_mmap.h │ │ ├── file_format_raw.h │ │ ├── file_forwards.h │ │ ├── file_interface.h │ │ ├── file_mapping.h │ │ ├── file_page.h │ │ ├── meta.h │ │ ├── stream.h │ │ ├── stream_algorithms.h │ │ ├── string_external.h │ │ └── string_mmap.h │ │ ├── gff_io.h │ │ ├── gff_io │ │ ├── INFO │ │ ├── gff_io_base.h │ │ ├── gff_io_context.h │ │ └── gff_stream.h │ │ ├── graph_algorithms.h │ │ ├── graph_algorithms │ │ ├── INFO │ │ ├── graph_algorithm.h │ │ ├── graph_algorithm_heap_tree.h │ │ ├── graph_algorithm_hmm.h │ │ └── graph_algorithm_lis_his.h │ │ ├── graph_align.h │ │ ├── graph_align │ │ ├── INFO │ │ ├── graph_algorithm_refine_align.h │ │ ├── graph_algorithm_refine_aligngraph.h │ │ ├── graph_algorithm_refine_annotation.h │ │ ├── graph_algorithm_refine_exact.h │ │ ├── graph_algorithm_refine_exact_iterative.h │ │ ├── graph_algorithm_refine_fragment.h │ │ ├── graph_algorithm_refine_inexact.h │ │ ├── graph_algorithm_refine_scoring.h │ │ ├── graph_impl_align.h │ │ └── graph_impl_align_adapt.h │ │ ├── graph_types.h │ │ ├── graph_types │ │ ├── INFO │ │ ├── graph_base.h │ │ ├── graph_drawing.h │ │ ├── graph_edgestump.h │ │ ├── graph_idmanager.h │ │ ├── graph_impl_automaton.h │ │ ├── graph_impl_directed.h │ │ ├── graph_impl_fragment.h │ │ ├── graph_impl_hmm.h │ │ ├── graph_impl_oracle.h │ │ ├── graph_impl_tree.h │ │ ├── graph_impl_trie.h │ │ ├── graph_impl_undirected.h │ │ ├── graph_impl_wordgraph.h │ │ ├── graph_interface.h │ │ ├── graph_iterator.h │ │ ├── graph_iterator_adjacency.h │ │ ├── graph_iterator_bfs.h │ │ ├── graph_iterator_dfs.h │ │ ├── graph_iterator_edge.h │ │ ├── graph_iterator_outedge.h │ │ ├── graph_iterator_vertex.h │ │ ├── graph_property.h │ │ └── graph_utility_parsing.h │ │ ├── misc │ │ ├── misc_interval_tree.h │ │ ├── misc_memset.h │ │ ├── misc_name_store_cache.h │ │ ├── misc_parsing.h │ │ ├── misc_union_find.h │ │ ├── priority_type_base.h │ │ └── priority_type_heap.h │ │ ├── modifier.h │ │ ├── modifier │ │ ├── INFO │ │ ├── modifier_alphabet.h │ │ ├── modifier_alphabet_expansion.h │ │ ├── modifier_functors.h │ │ ├── modifier_iterator.h │ │ ├── modifier_reverse.h │ │ ├── modifier_shortcuts.h │ │ ├── modifier_string.h │ │ └── modifier_view.h │ │ ├── parallel.h │ │ ├── parallel │ │ ├── INFO │ │ ├── parallel_algorithms.h │ │ ├── parallel_atomic_misc.h │ │ ├── parallel_atomic_primitives.h │ │ ├── parallel_macros.h │ │ ├── parallel_splitting.h │ │ └── parallel_tags.h │ │ ├── platform.h │ │ ├── platform │ │ ├── INFO │ │ ├── platform_gcc.h │ │ ├── platform_icc.h │ │ ├── platform_mingw.h │ │ ├── platform_pgi.h │ │ ├── platform_solaris.h │ │ ├── platform_windows.h │ │ └── windows_stdint.h │ │ ├── random.h │ │ ├── random │ │ ├── INFO │ │ ├── ext_MersenneTwister.h │ │ ├── random_base.h │ │ ├── random_beta.h │ │ ├── random_beta_kfunc.h │ │ ├── random_geometric.h │ │ ├── random_lognormal.h │ │ ├── random_mt19937.h │ │ ├── random_normal.h │ │ ├── random_rng_functor.h │ │ ├── random_shuffle.h │ │ └── random_uniform.h │ │ ├── score.h │ │ ├── score │ │ ├── INFO │ │ ├── score_base.h │ │ ├── score_edit.h │ │ ├── score_matrix.h │ │ ├── score_matrix_data.h │ │ ├── score_matrix_io.h │ │ └── score_simple.h │ │ ├── seq_io.h │ │ ├── seq_io │ │ ├── INFO │ │ ├── fai_index.h │ │ ├── genomic_region.h │ │ ├── guess_stream_format.h │ │ ├── read_embl.h │ │ ├── read_fasta_fastq.h │ │ ├── read_genbank.h │ │ ├── sequence_stream.h │ │ ├── sequence_stream_impl.h │ │ ├── simple_read_fasta.h │ │ └── write_fasta_fastq.h │ │ ├── sequence.h │ │ ├── sequence │ │ ├── INFO │ │ ├── adapt_array_pointer.h │ │ ├── adapt_std_list.h │ │ ├── adapt_std_string.h │ │ ├── adapt_std_vector.h │ │ ├── iter_concat_virtual.h │ │ ├── segment_base.h │ │ ├── segment_infix.h │ │ ├── segment_prefix.h │ │ ├── segment_suffix.h │ │ ├── segment_utils.h │ │ ├── sequence_concatenator.h │ │ ├── sequence_forwards.h │ │ ├── sequence_interface.h │ │ ├── sequence_lexical.h │ │ ├── sequence_shortcuts.h │ │ ├── string_alloc.h │ │ ├── string_array.h │ │ ├── string_base.h │ │ ├── string_block.h │ │ ├── string_cstyle.h │ │ ├── string_packed.h │ │ ├── string_set_base.h │ │ ├── string_set_concat_direct.h │ │ ├── string_set_dependent_generous.h │ │ ├── string_set_dependent_tight.h │ │ └── string_set_owner.h │ │ ├── store.h │ │ ├── store │ │ ├── INFO │ │ ├── store_align.h │ │ ├── store_align_intervals.h │ │ ├── store_all.h │ │ ├── store_annotation.h │ │ ├── store_base.h │ │ ├── store_contig.h │ │ ├── store_intervaltree.h │ │ ├── store_io.h │ │ ├── store_io_gff.h │ │ ├── store_io_sam.h │ │ ├── store_io_ucsc.h │ │ ├── store_library.h │ │ ├── store_matepair.h │ │ └── store_read.h │ │ ├── stream.h │ │ ├── stream │ │ ├── INFO │ │ ├── adapt_cstdio.h │ │ ├── adapt_fstream.h │ │ ├── adapt_iostream.h │ │ ├── adapt_mmap.h │ │ ├── adapt_sstream.h │ │ ├── concept_stream.h │ │ ├── is.h │ │ ├── lexical_cast.h │ │ ├── read.h │ │ ├── read_auto_format.h │ │ ├── read_sam.h │ │ ├── record_reader_base.h │ │ ├── record_reader_double.h │ │ ├── record_reader_double_mmap.h │ │ ├── record_reader_single.h │ │ ├── record_reader_single_mmap.h │ │ ├── stream_base.h │ │ ├── stream_bgzf.h │ │ ├── stream_bz2_file.h │ │ ├── stream_char_array.h │ │ ├── stream_gz_file.h │ │ ├── tokenize.h │ │ └── write.h │ │ ├── system.h │ │ └── system │ │ ├── INFO │ │ ├── file_async.h │ │ ├── file_directory.h │ │ ├── file_forwards.h │ │ ├── file_sync.h │ │ ├── system_base.h │ │ ├── system_event.h │ │ ├── system_forwards.h │ │ ├── system_mutex.h │ │ ├── system_sema.h │ │ └── system_thread.h ├── smhasher │ ├── MurmurHash3.cc │ └── MurmurHash3.h └── zlib │ ├── .gitignore │ ├── CMakeLists.txt │ ├── ChangeLog │ ├── FAQ │ ├── INDEX │ ├── Makefile.in │ ├── Makefile.pic │ ├── README │ ├── adler32.c │ ├── compress.c │ ├── configure │ ├── crc32.c │ ├── crc32.h │ ├── deflate.c │ ├── deflate.h │ ├── doc │ ├── algorithm.txt │ ├── rfc1950.txt │ ├── rfc1951.txt │ ├── rfc1952.txt │ └── txtvsbin.txt │ ├── gzclose.c │ ├── gzguts.h │ ├── gzlib.c │ ├── gzread.c │ ├── gzwrite.c │ ├── infback.c │ ├── inffast.c │ ├── inffast.h │ ├── inffixed.h │ ├── inflate.c │ ├── inflate.h │ ├── inftrees.c │ ├── inftrees.h │ ├── make_vms.com │ ├── test │ ├── example.c │ ├── infcover.c │ └── minigzip.c │ ├── treebuild.xml │ ├── trees.c │ ├── trees.h │ ├── uncompr.c │ ├── win32 │ ├── DLL_FAQ.txt │ ├── Makefile.bor │ ├── Makefile.gcc │ ├── Makefile.msc │ ├── README-WIN32.txt │ ├── VisualC.txt │ ├── zlib.def │ └── zlib1.rc │ ├── zconf.h.cmakein │ ├── zconf.h.in │ ├── zlib.3 │ ├── zlib.3.pdf │ ├── zlib.h │ ├── zlib.map │ ├── 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