MANIFEST.in
requirements.txt
setup.cfg
setup.py
mccortex/.gitignore
mccortex/.gitmodules
mccortex/.travis.yml
mccortex/AUTHORS
mccortex/LICENSE
mccortex/Makefile
mccortex/README.md
mccortex/.git/COMMIT_EDITMSG
mccortex/.git/FETCH_HEAD
mccortex/.git/HEAD
mccortex/.git/ORIG_HEAD
mccortex/.git/config
mccortex/.git/config~
mccortex/.git/description
mccortex/.git/index
mccortex/.git/packed-refs
mccortex/.git/hooks/applypatch-msg.sample
mccortex/.git/hooks/commit-msg.sample
mccortex/.git/hooks/post-commit.sample
mccortex/.git/hooks/post-receive.sample
mccortex/.git/hooks/post-update.sample
mccortex/.git/hooks/pre-applypatch.sample
mccortex/.git/hooks/pre-commit.sample
mccortex/.git/hooks/pre-rebase.sample
mccortex/.git/hooks/prepare-commit-msg.sample
mccortex/.git/hooks/update.sample
mccortex/.git/info/exclude
mccortex/.git/logs/HEAD
mccortex/.git/logs/refs/heads/geno
mccortex/.git/logs/refs/heads/genotype
mccortex/.git/logs/refs/heads/master
mccortex/.git/logs/refs/remotes/origin/genotype
mccortex/.git/objects/0f/0b8cd1d561ade700364f669f0d736f37d874b2
mccortex/.git/objects/22/410eacc3c416c73dec86a133f063cf1405663e
mccortex/.git/objects/2b/5aa3b7beda9da62625f0d9722e02202860fb60
mccortex/.git/objects/47/3d552624f5812c3612708db2c2d3e33863796d
mccortex/.git/objects/8b/64fd25504796ef0a20f954957d63aa2736ef66
mccortex/.git/objects/pack/pack-4c13dfcbeaa5e302c66352c85d5ff5a9d5ad2a3e.idx
mccortex/.git/objects/pack/pack-4c13dfcbeaa5e302c66352c85d5ff5a9d5ad2a3e.pack
mccortex/.git/refs/heads/geno
mccortex/.git/refs/heads/genotype
mccortex/.git/refs/heads/master
mccortex/.git/refs/remotes/origin/HEAD
mccortex/.git/refs/remotes/origin/genotype
mccortex/benchmark/calling-comparison.mk
mccortex/benchmark/10diploid10X/run-sim.sh
mccortex/benchmark/10diploid10X/smaller.fa
mccortex/benchmark/diploid60X/run-sim.sh
mccortex/benchmark/minidiploid/run-sim.sh
mccortex/benchmark/paperSimulations/Makefile
mccortex/benchmark/paperSimulations/README
mccortex/bin/mccortex31
mccortex/build/alignment31/correct_alignment.o
mccortex/build/alignment31/correct_aln_input.o
mccortex/build/alignment31/correct_aln_stats.o
mccortex/build/alignment31/db_alignment.o
mccortex/build/basic/aligned_call.o
mccortex/build/basic/async_read_io.o
mccortex/build/basic/binary_seq.o
mccortex/build/basic/call_file_reader.o
mccortex/build/basic/chrom_pos_list.o
mccortex/build/basic/cmd.o
mccortex/build/basic/decomp_breakpoint.o
mccortex/build/basic/decomp_bubble.o
mccortex/build/basic/dna.o
mccortex/build/basic/file_filter.o
mccortex/build/basic/file_util.o
mccortex/build/basic/graph_info.o
mccortex/build/basic/hash_mem.o
mccortex/build/basic/range.o
mccortex/build/basic/seq_loading_stats.o
mccortex/build/basic/seq_reader.o
mccortex/build/basic/seqout.o
mccortex/build/basic/str_parsing.o
mccortex/build/commands31/ctx_breakpoints.o
mccortex/build/commands31/ctx_bubbles.o
mccortex/build/commands31/ctx_build.o
mccortex/build/commands31/ctx_calls2vcf.o
mccortex/build/commands31/ctx_clean.o
mccortex/build/commands31/ctx_contigs.o
mccortex/build/commands31/ctx_correct.o
mccortex/build/commands31/ctx_coverage.o
mccortex/build/commands31/ctx_dist_matrix.o
mccortex/build/commands31/ctx_exp_abc.o
mccortex/build/commands31/ctx_exp_hashtest.o
mccortex/build/commands31/ctx_geno.o
mccortex/build/commands31/ctx_health_check.o
mccortex/build/commands31/ctx_index.o
mccortex/build/commands31/ctx_infer_edges.o
mccortex/build/commands31/ctx_join.o
mccortex/build/commands31/ctx_links.o
mccortex/build/commands31/ctx_pjoin.o
mccortex/build/commands31/ctx_pop_bubbles.o
mccortex/build/commands31/ctx_pview.o
mccortex/build/commands31/ctx_reads.o
mccortex/build/commands31/ctx_rmsubstr.o
mccortex/build/commands31/ctx_server.o
mccortex/build/commands31/ctx_sort.o
mccortex/build/commands31/ctx_subgraph.o
mccortex/build/commands31/ctx_thread.o
mccortex/build/commands31/ctx_uniqkmers.o
mccortex/build/commands31/ctx_unitigs.o
mccortex/build/commands31/ctx_vcfcov.o
mccortex/build/commands31/ctx_vcfgeno.o
mccortex/build/commands31/ctx_view.o
mccortex/build/commands31/read_thread_cmd.o
mccortex/build/global/ctx_alloc.o
mccortex/build/global/ctx_assert.o
mccortex/build/global/ctx_output.o
mccortex/build/global/global.o
mccortex/build/global/util.o
mccortex/build/graph31/binary_kmer.o
mccortex/build/graph31/cmd_mem.o
mccortex/build/graph31/contig_confidence.o
mccortex/build/graph31/db_graph.o
mccortex/build/graph31/db_node.o
mccortex/build/graph31/graph_cache.o
mccortex/build/graph31/graph_crawler.o
mccortex/build/graph31/graph_file_reader.o
mccortex/build/graph31/graph_format.o
mccortex/build/graph31/graph_step.o
mccortex/build/graph31/graph_walker.o
mccortex/build/graph31/graph_writer.o
mccortex/build/graph31/graphs_load.o
mccortex/build/graph31/hash_table.o
mccortex/build/graph31/json_hdr.o
mccortex/build/graph31/kmer_occur.o
mccortex/build/graph31/prune_nodes.o
mccortex/build/graph31/supernode.o
mccortex/build/graph31/unitig_graph.o
mccortex/build/graph31/vcf_misc.o
mccortex/build/graph_paths31/gpath_checks.o
mccortex/build/graph_paths31/gpath_reader.o
mccortex/build/graph_paths31/gpath_save.o
mccortex/build/kmer31/kmer_size.o
mccortex/build/paths/gpath.o
mccortex/build/paths/gpath_follow.o
mccortex/build/paths/gpath_hash.o
mccortex/build/paths/gpath_set.o
mccortex/build/paths/gpath_store.o
mccortex/build/paths/gpath_subset.o
mccortex/build/paths/link_tree.o
mccortex/build/tools31/assemble_contigs.o
mccortex/build/tools31/assemble_stats.o
mccortex/build/tools31/breakpoint_caller.o
mccortex/build/tools31/bubble_caller.o
mccortex/build/tools31/build_graph.o
mccortex/build/tools31/clean_graph.o
mccortex/build/tools31/correct_reads.o
mccortex/build/tools31/generate_paths.o
mccortex/build/tools31/genotyping.o
mccortex/build/tools31/infer_edges.o
mccortex/build/tools31/pop_bubbles.o
mccortex/build/tools31/subgraph.o
mccortex/build/tools31/vcf_coverage.o
mccortex/dev/bkmer_revcmp/Makefile
mccortex/dev/bkmer_revcmp/revcmp.c
mccortex/docs/file_formats/graph_file_format.txt
mccortex/docs/file_formats/graph_format_v7.txt
mccortex/docs/file_formats/paths_file_format.txt
mccortex/libs/Makefile
mccortex/libs/bcftools/.gitattributes
mccortex/libs/bcftools/.gitignore
mccortex/libs/bcftools/.travis.yml
mccortex/libs/bcftools/AUTHORS
mccortex/libs/bcftools/HMM.c
mccortex/libs/bcftools/HMM.h
mccortex/libs/bcftools/INSTALL
mccortex/libs/bcftools/LICENSE
mccortex/libs/bcftools/Makefile
mccortex/libs/bcftools/README
mccortex/libs/bcftools/README.md
mccortex/libs/bcftools/bcftools.h
mccortex/libs/bcftools/call.h
mccortex/libs/bcftools/ccall.c
mccortex/libs/bcftools/consensus.c
mccortex/libs/bcftools/convert.c
mccortex/libs/bcftools/convert.h
mccortex/libs/bcftools/em.c
mccortex/libs/bcftools/filter.c
mccortex/libs/bcftools/filter.h
mccortex/libs/bcftools/gvcf.c
mccortex/libs/bcftools/gvcf.h
mccortex/libs/bcftools/khash_str2str.h
mccortex/libs/bcftools/kmin.c
mccortex/libs/bcftools/kmin.h
mccortex/libs/bcftools/main.c
mccortex/libs/bcftools/mcall.c
mccortex/libs/bcftools/peakfit.c
mccortex/libs/bcftools/peakfit.h
mccortex/libs/bcftools/ploidy.c
mccortex/libs/bcftools/ploidy.h
mccortex/libs/bcftools/plot-vcfstats
mccortex/libs/bcftools/polysomy.c
mccortex/libs/bcftools/prob1.c
mccortex/libs/bcftools/prob1.h
mccortex/libs/bcftools/rbuf.h
mccortex/libs/bcftools/reheader.c
mccortex/libs/bcftools/tabix.c
mccortex/libs/bcftools/tsv2vcf.c
mccortex/libs/bcftools/tsv2vcf.h
mccortex/libs/bcftools/vcfannotate.c
mccortex/libs/bcftools/vcfcall.c
mccortex/libs/bcftools/vcfcnv.c
mccortex/libs/bcftools/vcfconcat.c
mccortex/libs/bcftools/vcfconvert.c
mccortex/libs/bcftools/vcffilter.c
mccortex/libs/bcftools/vcfgtcheck.c
mccortex/libs/bcftools/vcfindex.c
mccortex/libs/bcftools/vcfisec.c
mccortex/libs/bcftools/vcfmerge.c
mccortex/libs/bcftools/vcfnorm.c
mccortex/libs/bcftools/vcfplugin.c
mccortex/libs/bcftools/vcfquery.c
mccortex/libs/bcftools/vcfroh.c
mccortex/libs/bcftools/vcfsom.c
mccortex/libs/bcftools/vcfstats.c
mccortex/libs/bcftools/vcfutils.pl
mccortex/libs/bcftools/vcfview.c
mccortex/libs/bcftools/vcmp.c
mccortex/libs/bcftools/vcmp.h
mccortex/libs/bcftools/version.c
mccortex/libs/bcftools/.git/FETCH_HEAD
mccortex/libs/bcftools/.git/HEAD
mccortex/libs/bcftools/.git/config
mccortex/libs/bcftools/.git/description
mccortex/libs/bcftools/.git/index
mccortex/libs/bcftools/.git/packed-refs
mccortex/libs/bcftools/.git/hooks/applypatch-msg.sample
mccortex/libs/bcftools/.git/hooks/commit-msg.sample
mccortex/libs/bcftools/.git/hooks/post-commit.sample
mccortex/libs/bcftools/.git/hooks/post-receive.sample
mccortex/libs/bcftools/.git/hooks/post-update.sample
mccortex/libs/bcftools/.git/hooks/pre-applypatch.sample
mccortex/libs/bcftools/.git/hooks/pre-commit.sample
mccortex/libs/bcftools/.git/hooks/pre-rebase.sample
mccortex/libs/bcftools/.git/hooks/prepare-commit-msg.sample
mccortex/libs/bcftools/.git/hooks/update.sample
mccortex/libs/bcftools/.git/info/exclude
mccortex/libs/bcftools/.git/logs/HEAD
mccortex/libs/bcftools/.git/logs/refs/heads/develop
mccortex/libs/bcftools/.git/objects/pack/pack-d2f5f6251494d71e78199f7bc5cfae214a226fb2.idx
mccortex/libs/bcftools/.git/objects/pack/pack-d2f5f6251494d71e78199f7bc5cfae214a226fb2.pack
mccortex/libs/bcftools/.git/refs/heads/develop
mccortex/libs/bcftools/.git/refs/remotes/origin/HEAD
mccortex/libs/bcftools/.travis/clone
mccortex/libs/bcftools/doc/bcftools.1
mccortex/libs/bcftools/doc/bcftools.html
mccortex/libs/bcftools/doc/bcftools.txt
mccortex/libs/bcftools/doc/docbook-xsl.css
mccortex/libs/bcftools/plugins/color-chrs.c
mccortex/libs/bcftools/plugins/color-chrs.mk
mccortex/libs/bcftools/plugins/color-chrs.pl
mccortex/libs/bcftools/plugins/counts.c
mccortex/libs/bcftools/plugins/dosage.c
mccortex/libs/bcftools/plugins/fill-AN-AC.c
mccortex/libs/bcftools/plugins/fill-tags.c
mccortex/libs/bcftools/plugins/fixploidy.c
mccortex/libs/bcftools/plugins/fixploidy.mk
mccortex/libs/bcftools/plugins/frameshifts.c
mccortex/libs/bcftools/plugins/impute-info.c
mccortex/libs/bcftools/plugins/mendelian.c
mccortex/libs/bcftools/plugins/missing2ref.c
mccortex/libs/bcftools/plugins/setGT.c
mccortex/libs/bcftools/plugins/tag2tag.c
mccortex/libs/bcftools/plugins/vcf2sex.c
mccortex/libs/bcftools/plugins/vcf2sex.mk
mccortex/libs/bcftools/test/23andme.fa
mccortex/libs/bcftools/test/23andme.fa.fai
mccortex/libs/bcftools/test/annotate.hdr
mccortex/libs/bcftools/test/annotate.out
mccortex/libs/bcftools/test/annotate.tab
mccortex/libs/bcftools/test/annotate.vcf
mccortex/libs/bcftools/test/annotate2.out
mccortex/libs/bcftools/test/annotate2.tab
mccortex/libs/bcftools/test/annotate2.vcf
mccortex/libs/bcftools/test/annotate3.out
mccortex/libs/bcftools/test/annotate3.vcf
mccortex/libs/bcftools/test/annotate4.hdr
mccortex/libs/bcftools/test/annotate4.out
mccortex/libs/bcftools/test/annotate4.vcf
mccortex/libs/bcftools/test/annotate5.out
mccortex/libs/bcftools/test/annotate6.out
mccortex/libs/bcftools/test/annotate7.out
mccortex/libs/bcftools/test/annotate8.out
mccortex/libs/bcftools/test/annotate9.out
mccortex/libs/bcftools/test/annotate9.vcf
mccortex/libs/bcftools/test/annots.vcf
mccortex/libs/bcftools/test/annots2.vcf
mccortex/libs/bcftools/test/annots4.tab
mccortex/libs/bcftools/test/annots4.vcf
mccortex/libs/bcftools/test/annots9.tab
mccortex/libs/bcftools/test/annots9.vcf
mccortex/libs/bcftools/test/check.chk
mccortex/libs/bcftools/test/check.gs.chrom.gen
mccortex/libs/bcftools/test/check.gs.chrom.samples
mccortex/libs/bcftools/test/check.gs.vcfids.gen
mccortex/libs/bcftools/test/check.gs.vcfids.samples
mccortex/libs/bcftools/test/check.gs.vcfids_chrom.gen
mccortex/libs/bcftools/test/check.gs.vcfids_chrom.samples
mccortex/libs/bcftools/test/check.vcf
mccortex/libs/bcftools/test/check_merge.chk
mccortex/libs/bcftools/test/concat.1.a.vcf
mccortex/libs/bcftools/test/concat.1.b.vcf
mccortex/libs/bcftools/test/concat.1.bcf.out
mccortex/libs/bcftools/test/concat.1.vcf.out
mccortex/libs/bcftools/test/concat.2.a.vcf
mccortex/libs/bcftools/test/concat.2.b.vcf
mccortex/libs/bcftools/test/concat.2.bcf.out
mccortex/libs/bcftools/test/concat.2.vcf.out
mccortex/libs/bcftools/test/concat.3.0.vcf
mccortex/libs/bcftools/test/concat.3.a.vcf
mccortex/libs/bcftools/test/concat.3.b.vcf
mccortex/libs/bcftools/test/concat.3.bcf.out
mccortex/libs/bcftools/test/concat.3.c.vcf
mccortex/libs/bcftools/test/concat.3.d.vcf
mccortex/libs/bcftools/test/concat.3.e.vcf
mccortex/libs/bcftools/test/concat.3.f.vcf
mccortex/libs/bcftools/test/concat.3.vcf.out
mccortex/libs/bcftools/test/concat.4.bcf.out
mccortex/libs/bcftools/test/concat.4.vcf.out
mccortex/libs/bcftools/test/consensus.1.chain
mccortex/libs/bcftools/test/consensus.1.out
mccortex/libs/bcftools/test/consensus.2.chain
mccortex/libs/bcftools/test/consensus.2.out
mccortex/libs/bcftools/test/consensus.3.chain
mccortex/libs/bcftools/test/consensus.3.out
mccortex/libs/bcftools/test/consensus.4.chain
mccortex/libs/bcftools/test/consensus.4.out
mccortex/libs/bcftools/test/consensus.5.out
mccortex/libs/bcftools/test/consensus.fa
mccortex/libs/bcftools/test/consensus.tab
mccortex/libs/bcftools/test/consensus.vcf
mccortex/libs/bcftools/test/consensus2.1.out
mccortex/libs/bcftools/test/consensus2.2.out
mccortex/libs/bcftools/test/consensus2.fa
mccortex/libs/bcftools/test/consensus2.vcf
mccortex/libs/bcftools/test/convert.23andme
mccortex/libs/bcftools/test/convert.23andme.vcf
mccortex/libs/bcftools/test/convert.gs.gt.gen
mccortex/libs/bcftools/test/convert.gs.gt.samples
mccortex/libs/bcftools/test/convert.gs.pl.gen
mccortex/libs/bcftools/test/convert.gs.pl.samples
mccortex/libs/bcftools/test/convert.gt.noHead.vcf
mccortex/libs/bcftools/test/convert.gt.vcf
mccortex/libs/bcftools/test/convert.gvcf.out
mccortex/libs/bcftools/test/convert.gvcf.vcf
mccortex/libs/bcftools/test/convert.hls.gt.hap
mccortex/libs/bcftools/test/convert.hls.gt.legend
mccortex/libs/bcftools/test/convert.hls.gt.samples
mccortex/libs/bcftools/test/convert.hls.haps
mccortex/libs/bcftools/test/convert.hls.legend
mccortex/libs/bcftools/test/convert.hls.samples
mccortex/libs/bcftools/test/convert.hs.gt.hap
mccortex/libs/bcftools/test/convert.hs.gt.samples
mccortex/libs/bcftools/test/convert.hs.hap
mccortex/libs/bcftools/test/convert.hs.sample
mccortex/libs/bcftools/test/convert.vcf
mccortex/libs/bcftools/test/dosage.out
mccortex/libs/bcftools/test/empty.idx.out
mccortex/libs/bcftools/test/empty.idx_count.out
mccortex/libs/bcftools/test/empty.vcf
mccortex/libs/bcftools/test/ex1.gtf.gz
mccortex/libs/bcftools/test/ex2.vcf
mccortex/libs/bcftools/test/ex3.sam
mccortex/libs/bcftools/test/fill-AN-AC.out
mccortex/libs/bcftools/test/fill-tags.out
mccortex/libs/bcftools/test/filter.1.out
mccortex/libs/bcftools/test/filter.1.vcf
mccortex/libs/bcftools/test/filter.10.out
mccortex/libs/bcftools/test/filter.2.out
mccortex/libs/bcftools/test/filter.2.vcf
mccortex/libs/bcftools/test/filter.3.out
mccortex/libs/bcftools/test/filter.3.vcf
mccortex/libs/bcftools/test/filter.4.out
mccortex/libs/bcftools/test/filter.4.vcf
mccortex/libs/bcftools/test/filter.5.out
mccortex/libs/bcftools/test/filter.6.out
mccortex/libs/bcftools/test/filter.7.out
mccortex/libs/bcftools/test/filter.8.out
mccortex/libs/bcftools/test/filter.9.out
mccortex/libs/bcftools/test/fixploidy.out
mccortex/libs/bcftools/test/fixploidy.ploidy
mccortex/libs/bcftools/test/fixploidy.samples
mccortex/libs/bcftools/test/fixploidy.vcf
mccortex/libs/bcftools/test/gvcf.fa
mccortex/libs/bcftools/test/gvcf.fa.fai
mccortex/libs/bcftools/test/idx.out
mccortex/libs/bcftools/test/idx.vcf
mccortex/libs/bcftools/test/idx_count.out
mccortex/libs/bcftools/test/isec.a.vcf
mccortex/libs/bcftools/test/isec.ab.C.out
mccortex/libs/bcftools/test/isec.ab.any.out
mccortex/libs/bcftools/test/isec.ab.both.out
mccortex/libs/bcftools/test/isec.ab.flt.out
mccortex/libs/bcftools/test/isec.ab.out
mccortex/libs/bcftools/test/isec.b.vcf
mccortex/libs/bcftools/test/isec.tab
mccortex/libs/bcftools/test/isec.tab.out
mccortex/libs/bcftools/test/large_chrom.20.1.2147483647.out
mccortex/libs/bcftools/test/large_chrom_csi_limit.20.1.2147483647.out
mccortex/libs/bcftools/test/large_chrom_csi_limit.vcf
mccortex/libs/bcftools/test/large_chrom_tbi_limit.20.1.536870912.out
mccortex/libs/bcftools/test/large_chrom_tbi_limit.vcf
mccortex/libs/bcftools/test/many.alleles.trim.out
mccortex/libs/bcftools/test/many.alleles.vcf
mccortex/libs/bcftools/test/merge.2.a.vcf
mccortex/libs/bcftools/test/merge.2.all.out
mccortex/libs/bcftools/test/merge.2.b.vcf
mccortex/libs/bcftools/test/merge.2.both.out
mccortex/libs/bcftools/test/merge.2.none.out
mccortex/libs/bcftools/test/merge.3.a.vcf
mccortex/libs/bcftools/test/merge.3.b.vcf
mccortex/libs/bcftools/test/merge.3.out
mccortex/libs/bcftools/test/merge.4.a.vcf
mccortex/libs/bcftools/test/merge.4.b.vcf
mccortex/libs/bcftools/test/merge.4.out
mccortex/libs/bcftools/test/merge.a.chk
mccortex/libs/bcftools/test/merge.a.vcf
mccortex/libs/bcftools/test/merge.abc.out
mccortex/libs/bcftools/test/merge.b.vcf
mccortex/libs/bcftools/test/merge.c.vcf
mccortex/libs/bcftools/test/missing.vcf
mccortex/libs/bcftools/test/missing2ref.out
mccortex/libs/bcftools/test/mpileup.1.out
mccortex/libs/bcftools/test/mpileup.2.out
mccortex/libs/bcftools/test/mpileup.X.out
mccortex/libs/bcftools/test/mpileup.X.vcf
mccortex/libs/bcftools/test/mpileup.c.1.out
mccortex/libs/bcftools/test/mpileup.c.X.out
mccortex/libs/bcftools/test/mpileup.cAls.out
mccortex/libs/bcftools/test/mpileup.ped
mccortex/libs/bcftools/test/mpileup.ploidy
mccortex/libs/bcftools/test/mpileup.samples
mccortex/libs/bcftools/test/mpileup.tab
mccortex/libs/bcftools/test/mpileup.vcf
mccortex/libs/bcftools/test/norm.fa
mccortex/libs/bcftools/test/norm.fa.fai
mccortex/libs/bcftools/test/norm.merge.2.out
mccortex/libs/bcftools/test/norm.merge.2.vcf
mccortex/libs/bcftools/test/norm.merge.3.out
mccortex/libs/bcftools/test/norm.merge.3.vcf
mccortex/libs/bcftools/test/norm.merge.out
mccortex/libs/bcftools/test/norm.merge.strict.out
mccortex/libs/bcftools/test/norm.merge.vcf
mccortex/libs/bcftools/test/norm.out
mccortex/libs/bcftools/test/norm.setref.out
mccortex/libs/bcftools/test/norm.setref.vcf
mccortex/libs/bcftools/test/norm.split.2.out
mccortex/libs/bcftools/test/norm.split.2.vcf
mccortex/libs/bcftools/test/norm.split.and.norm.out
mccortex/libs/bcftools/test/norm.split.out
mccortex/libs/bcftools/test/norm.split.vcf
mccortex/libs/bcftools/test/norm.vcf
mccortex/libs/bcftools/test/plugin-missing2ref.out.vcf
mccortex/libs/bcftools/test/plugin-missing2ref.vcf
mccortex/libs/bcftools/test/plugin1.vcf
mccortex/libs/bcftools/test/query.10.out
mccortex/libs/bcftools/test/query.11.out
mccortex/libs/bcftools/test/query.12.out
mccortex/libs/bcftools/test/query.13.out
mccortex/libs/bcftools/test/query.14.out
mccortex/libs/bcftools/test/query.15.out
mccortex/libs/bcftools/test/query.16.out
mccortex/libs/bcftools/test/query.17.out
mccortex/libs/bcftools/test/query.18.out
mccortex/libs/bcftools/test/query.19.out
mccortex/libs/bcftools/test/query.2.out
mccortex/libs/bcftools/test/query.2.vcf
mccortex/libs/bcftools/test/query.20.out
mccortex/libs/bcftools/test/query.21.out
mccortex/libs/bcftools/test/query.22.out
mccortex/libs/bcftools/test/query.23.out
mccortex/libs/bcftools/test/query.3.out
mccortex/libs/bcftools/test/query.4.out
mccortex/libs/bcftools/test/query.5.out
mccortex/libs/bcftools/test/query.6.out
mccortex/libs/bcftools/test/query.7.out
mccortex/libs/bcftools/test/query.8.out
mccortex/libs/bcftools/test/query.9.out
mccortex/libs/bcftools/test/query.filter.vcf
mccortex/libs/bcftools/test/query.out
mccortex/libs/bcftools/test/query.vcf
mccortex/libs/bcftools/test/regions.out
mccortex/libs/bcftools/test/regions.tab
mccortex/libs/bcftools/test/regions.vcf
mccortex/libs/bcftools/test/reheader.1.out
mccortex/libs/bcftools/test/reheader.1.out.bcf
mccortex/libs/bcftools/test/reheader.2.out
mccortex/libs/bcftools/test/reheader.hdr
mccortex/libs/bcftools/test/reheader.samples
mccortex/libs/bcftools/test/reheader.samples2
mccortex/libs/bcftools/test/reheader.vcf
mccortex/libs/bcftools/test/stats.a.vcf
mccortex/libs/bcftools/test/stats.b.vcf
mccortex/libs/bcftools/test/stats.chk
mccortex/libs/bcftools/test/tabix.1.3000151.out
mccortex/libs/bcftools/test/tabix.2.3199812.out
mccortex/libs/bcftools/test/test-rbuf.c
mccortex/libs/bcftools/test/test.pl
mccortex/libs/bcftools/test/vcf2sex.out
mccortex/libs/bcftools/test/vcf2sex.vcf
mccortex/libs/bcftools/test/view.1.out
mccortex/libs/bcftools/test/view.10.out
mccortex/libs/bcftools/test/view.2.out
mccortex/libs/bcftools/test/view.3.out
mccortex/libs/bcftools/test/view.4.out
mccortex/libs/bcftools/test/view.5.out
mccortex/libs/bcftools/test/view.6.out
mccortex/libs/bcftools/test/view.7.out
mccortex/libs/bcftools/test/view.8.out
mccortex/libs/bcftools/test/view.9.out
mccortex/libs/bcftools/test/view.GL.vcf
mccortex/libs/bcftools/test/view.PL.vcf
mccortex/libs/bcftools/test/view.chrs.out
mccortex/libs/bcftools/test/view.chrs.tab
mccortex/libs/bcftools/test/view.chrs.vcf
mccortex/libs/bcftools/test/view.dropgenotypes.noheader.out
mccortex/libs/bcftools/test/view.dropgenotypes.out
mccortex/libs/bcftools/test/view.exclude.out
mccortex/libs/bcftools/test/view.filter.1.out
mccortex/libs/bcftools/test/view.filter.10.out
mccortex/libs/bcftools/test/view.filter.11.out
mccortex/libs/bcftools/test/view.filter.2.out
mccortex/libs/bcftools/test/view.filter.3.out
mccortex/libs/bcftools/test/view.filter.4.out
mccortex/libs/bcftools/test/view.filter.5.out
mccortex/libs/bcftools/test/view.filter.6.out
mccortex/libs/bcftools/test/view.filter.7.out
mccortex/libs/bcftools/test/view.filter.8.out
mccortex/libs/bcftools/test/view.filter.9.out
mccortex/libs/bcftools/test/view.filter.annovar.1.out
mccortex/libs/bcftools/test/view.filter.annovar.2.out
mccortex/libs/bcftools/test/view.filter.annovar.3.out
mccortex/libs/bcftools/test/view.filter.annovar.vcf
mccortex/libs/bcftools/test/view.filter.vcf
mccortex/libs/bcftools/test/view.minmaxac.1.out
mccortex/libs/bcftools/test/view.minmaxac.2.out
mccortex/libs/bcftools/test/view.minmaxac.vcf
mccortex/libs/bcftools/test/view.omitgenotypes.out
mccortex/libs/bcftools/test/view.omitgenotypes.vcf
mccortex/libs/bcftools/test/view.vcf
mccortex/libs/bcftools/test/view.vectors.A.out
mccortex/libs/bcftools/test/view.vectors.B.out
mccortex/libs/bcftools/test/view.vectors.vcf
mccortex/libs/biogrok/README.md
mccortex/libs/biogrok/ascii-chr
mccortex/libs/biogrok/ascii-ord
mccortex/libs/biogrok/bam-sample
mccortex/libs/biogrok/dna-key
mccortex/libs/biogrok/dna-revcmp
mccortex/libs/biogrok/hist-data
mccortex/libs/biogrok/mem-jobs
mccortex/libs/biogrok/mem-rss
mccortex/libs/biogrok/mem-vsize
mccortex/libs/biogrok/mem2str
mccortex/libs/biogrok/num2str
mccortex/libs/biogrok/sam-count
mccortex/libs/biogrok/sam-entries
mccortex/libs/biogrok/sam-header
mccortex/libs/biogrok/strcasecmp
mccortex/libs/biogrok/strcmp
mccortex/libs/biogrok/strlc
mccortex/libs/biogrok/strlen
mccortex/libs/biogrok/strrev
mccortex/libs/biogrok/struc
mccortex/libs/biogrok/vcf-add-contigs
mccortex/libs/biogrok/vcf-count
mccortex/libs/biogrok/vcf-count-alleles
mccortex/libs/biogrok/vcf-entries
mccortex/libs/biogrok/vcf-fail
mccortex/libs/biogrok/vcf-header
mccortex/libs/biogrok/vcf-order
mccortex/libs/biogrok/vcf-pass
mccortex/libs/biogrok/vcf-rename
mccortex/libs/biogrok/vcf-sample-rename
mccortex/libs/biogrok/vcf-sort
mccortex/libs/biogrok/.git/FETCH_HEAD
mccortex/libs/biogrok/.git/HEAD
mccortex/libs/biogrok/.git/config
mccortex/libs/biogrok/.git/description
mccortex/libs/biogrok/.git/index
mccortex/libs/biogrok/.git/packed-refs
mccortex/libs/biogrok/.git/hooks/applypatch-msg.sample
mccortex/libs/biogrok/.git/hooks/commit-msg.sample
mccortex/libs/biogrok/.git/hooks/post-commit.sample
mccortex/libs/biogrok/.git/hooks/post-receive.sample
mccortex/libs/biogrok/.git/hooks/post-update.sample
mccortex/libs/biogrok/.git/hooks/pre-applypatch.sample
mccortex/libs/biogrok/.git/hooks/pre-commit.sample
mccortex/libs/biogrok/.git/hooks/pre-rebase.sample
mccortex/libs/biogrok/.git/hooks/prepare-commit-msg.sample
mccortex/libs/biogrok/.git/hooks/update.sample
mccortex/libs/biogrok/.git/info/exclude
mccortex/libs/biogrok/.git/logs/HEAD
mccortex/libs/biogrok/.git/logs/refs/heads/master
mccortex/libs/biogrok/.git/objects/pack/pack-d64b5adb0f89341bebf333290b16708d24ccd0b8.idx
mccortex/libs/biogrok/.git/objects/pack/pack-d64b5adb0f89341bebf333290b16708d24ccd0b8.pack
mccortex/libs/biogrok/.git/refs/heads/master
mccortex/libs/biogrok/.git/refs/remotes/origin/HEAD
mccortex/libs/bioinf-perl/README
mccortex/libs/bioinf-perl/.git/FETCH_HEAD
mccortex/libs/bioinf-perl/.git/HEAD
mccortex/libs/bioinf-perl/.git/config
mccortex/libs/bioinf-perl/.git/description
mccortex/libs/bioinf-perl/.git/index
mccortex/libs/bioinf-perl/.git/packed-refs
mccortex/libs/bioinf-perl/.git/hooks/applypatch-msg.sample
mccortex/libs/bioinf-perl/.git/hooks/commit-msg.sample
mccortex/libs/bioinf-perl/.git/hooks/post-commit.sample
mccortex/libs/bioinf-perl/.git/hooks/post-receive.sample
mccortex/libs/bioinf-perl/.git/hooks/post-update.sample
mccortex/libs/bioinf-perl/.git/hooks/pre-applypatch.sample
mccortex/libs/bioinf-perl/.git/hooks/pre-commit.sample
mccortex/libs/bioinf-perl/.git/hooks/pre-rebase.sample
mccortex/libs/bioinf-perl/.git/hooks/prepare-commit-msg.sample
mccortex/libs/bioinf-perl/.git/hooks/update.sample
mccortex/libs/bioinf-perl/.git/info/exclude
mccortex/libs/bioinf-perl/.git/logs/HEAD
mccortex/libs/bioinf-perl/.git/logs/refs/heads/master
mccortex/libs/bioinf-perl/.git/objects/pack/pack-e255e9f38749029eaeb3213f955e45ef675c7f30.idx
mccortex/libs/bioinf-perl/.git/objects/pack/pack-e255e9f38749029eaeb3213f955e45ef675c7f30.pack
mccortex/libs/bioinf-perl/.git/refs/heads/master
mccortex/libs/bioinf-perl/.git/refs/remotes/origin/HEAD
mccortex/libs/bioinf-perl/blast_scripts/blast_filter.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_aligned_reads.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_filter_covg_file_by_genes.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_filter_covgs.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_indel_sizes.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_memory.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_power.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_snp_count.pl
mccortex/libs/bioinf-perl/cortex_scripts/cortex_snp_tstv.pl
mccortex/libs/bioinf-perl/cortex_scripts/make_5p_flank_file.pl
mccortex/libs/bioinf-perl/cortex_scripts/make_branch_file.pl
mccortex/libs/bioinf-perl/cortex_scripts/print_5p_flank.pl
mccortex/libs/bioinf-perl/cortex_scripts/test_read_align.pl
mccortex/libs/bioinf-perl/de_bruijn/plot_debruijn.pl
mccortex/libs/bioinf-perl/de_bruijn/print_kmer_edges.pl
mccortex/libs/bioinf-perl/fastn_scripts/contig_stats.pl
mccortex/libs/bioinf-perl/fastn_scripts/fasta_acgtn.pl
mccortex/libs/bioinf-perl/fastn_scripts/fasta_clean.pl
mccortex/libs/bioinf-perl/fastn_scripts/fasta_shuffle.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_diff.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_gc.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_kmers.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_lengths.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_revcmp.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_select.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_sort.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_split.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_substr.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_total_length.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastn_wrap.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastq2fasta.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastq_qualities.pl
mccortex/libs/bioinf-perl/fastn_scripts/fastq_size.pl
mccortex/libs/bioinf-perl/genetics/codons_to_dna.pl
mccortex/libs/bioinf-perl/genetics/rev_comp.pl
mccortex/libs/bioinf-perl/genetics/rnd_seq.pl
mccortex/libs/bioinf-perl/genetics/seq_comp.pl
mccortex/libs/bioinf-perl/genetics/seq_rev.pl
mccortex/libs/bioinf-perl/genetics/split_rmsk.pl
mccortex/libs/bioinf-perl/lib/BLASTFile.pm
mccortex/libs/bioinf-perl/lib/CortexCovgFile.pm
mccortex/libs/bioinf-perl/lib/CortexGraph.pm
mccortex/libs/bioinf-perl/lib/FASTNFile.pm
mccortex/libs/bioinf-perl/lib/FastStat.pm
mccortex/libs/bioinf-perl/lib/GeneticsModule.pm
mccortex/libs/bioinf-perl/lib/IndexedString.pm
mccortex/libs/bioinf-perl/lib/IntervalList.pm
mccortex/libs/bioinf-perl/lib/IntervalTree.pm
mccortex/libs/bioinf-perl/lib/RefGenome.pm
mccortex/libs/bioinf-perl/lib/RepeatMaskerFile.pm
mccortex/libs/bioinf-perl/lib/UsefulModule.pm
mccortex/libs/bioinf-perl/lib/VCFFile.pm
mccortex/libs/bioinf-perl/sam_scripts/sam_filter_by_ref.pl
mccortex/libs/bioinf-perl/sam_scripts/sam_flags.pl
mccortex/libs/bioinf-perl/sim_mutations/README
mccortex/libs/bioinf-perl/sim_mutations/SimLib.pm
mccortex/libs/bioinf-perl/sim_mutations/block_to_brkpnts.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_breakpoints.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_bubble_vcf.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_compare.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_corrected.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_mutations.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_reads.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_substrings.pl
mccortex/libs/bioinf-perl/sim_mutations/sim_vcf.pl
mccortex/libs/bioinf-perl/utilities/gene_table_filter.pl
mccortex/libs/bioinf-perl/utilities/hist-matrix.pl
mccortex/libs/bioinf-perl/utilities/md5check.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_allele_freq.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_ancestral.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_ensgene.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_flanks.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_ins_del_tags.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_rmsk.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_add_rmsk_distance.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_align.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_chrom_distrib.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_combine_alleles.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_correct_strand.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_count_entries.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_count_info_tags.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_dist_from_genes.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_by_homopolymer.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_by_info.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_by_ref.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_by_regions.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_column.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_ins_del.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_tandem.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_filter_variants.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_header.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_header_add_contigs.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_isec.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_print.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_print_breakpoint.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_print_fasta.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_print_info_tags.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_print_svlen.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_remove_dupes.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_remove_overlaps.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_sample.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_sample_names.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_shuffle.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_snp_tstv.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_sort.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_split_inside_chrom.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_sum_svlens.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_summary.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_to_csv.pl
mccortex/libs/bioinf-perl/vcf_scripts/vcf_view.pl
mccortex/libs/bit_array/.gitignore
mccortex/libs/bit_array/.travis.yml
mccortex/libs/bit_array/AUTHORS
mccortex/libs/bit_array/LICENSE
mccortex/libs/bit_array/Makefile
mccortex/libs/bit_array/README.md
mccortex/libs/bit_array/bar.h
mccortex/libs/bit_array/bit_array.c
mccortex/libs/bit_array/bit_array.h
mccortex/libs/bit_array/bit_array.o
mccortex/libs/bit_array/bit_macros.h
mccortex/libs/bit_array/libbitarr.a
mccortex/libs/bit_array/.git/FETCH_HEAD
mccortex/libs/bit_array/.git/HEAD
mccortex/libs/bit_array/.git/config
mccortex/libs/bit_array/.git/description
mccortex/libs/bit_array/.git/index
mccortex/libs/bit_array/.git/packed-refs
mccortex/libs/bit_array/.git/hooks/applypatch-msg.sample
mccortex/libs/bit_array/.git/hooks/commit-msg.sample
mccortex/libs/bit_array/.git/hooks/post-commit.sample
mccortex/libs/bit_array/.git/hooks/post-receive.sample
mccortex/libs/bit_array/.git/hooks/post-update.sample
mccortex/libs/bit_array/.git/hooks/pre-applypatch.sample
mccortex/libs/bit_array/.git/hooks/pre-commit.sample
mccortex/libs/bit_array/.git/hooks/pre-rebase.sample
mccortex/libs/bit_array/.git/hooks/prepare-commit-msg.sample
mccortex/libs/bit_array/.git/hooks/update.sample
mccortex/libs/bit_array/.git/info/exclude
mccortex/libs/bit_array/.git/logs/HEAD
mccortex/libs/bit_array/.git/logs/refs/heads/master
mccortex/libs/bit_array/.git/objects/pack/pack-727b4cea6b299cc3473e2d2ae8fe0053af5b9e66.idx
mccortex/libs/bit_array/.git/objects/pack/pack-727b4cea6b299cc3473e2d2ae8fe0053af5b9e66.pack
mccortex/libs/bit_array/.git/refs/heads/master
mccortex/libs/bit_array/.git/refs/remotes/origin/HEAD
mccortex/libs/bit_array/dev/Makefile
mccortex/libs/bit_array/dev/bit_array_generate
mccortex/libs/bit_array/dev/bit_array_generate.c
mccortex/libs/bit_array/dev/bit_array_test
mccortex/libs/bit_array/dev/bit_array_test.c
mccortex/libs/bit_array/dev/bitlock_test
mccortex/libs/bit_array/dev/bitlock_test.c
mccortex/libs/bit_array/dev/bitlock_try_test
mccortex/libs/bit_array/dev/bitlock_try_test.c
mccortex/libs/bit_array/examples/Makefile
mccortex/libs/bit_array/examples/example.c
mccortex/libs/bit_array/examples/example.cpp
mccortex/libs/bit_array/examples/example_c
mccortex/libs/bit_array/examples/example_cpp
mccortex/libs/bwa/.gitignore
mccortex/libs/bwa/.travis.yml
mccortex/libs/bwa/COPYING
mccortex/libs/bwa/ChangeLog
mccortex/libs/bwa/Makefile
mccortex/libs/bwa/NEWS.md
mccortex/libs/bwa/QSufSort.c
mccortex/libs/bwa/QSufSort.h
mccortex/libs/bwa/README-alt.md
mccortex/libs/bwa/README.md
mccortex/libs/bwa/bamlite.c
mccortex/libs/bwa/bamlite.h
mccortex/libs/bwa/bntseq.c
mccortex/libs/bwa/bntseq.h
mccortex/libs/bwa/bwa.1
mccortex/libs/bwa/bwa.c
mccortex/libs/bwa/bwa.h
mccortex/libs/bwa/bwamem.c
mccortex/libs/bwa/bwamem.h
mccortex/libs/bwa/bwamem_extra.c
mccortex/libs/bwa/bwamem_pair.c
mccortex/libs/bwa/bwape.c
mccortex/libs/bwa/bwase.c
mccortex/libs/bwa/bwase.h
mccortex/libs/bwa/bwaseqio.c
mccortex/libs/bwa/bwashm.c
mccortex/libs/bwa/bwt.c
mccortex/libs/bwa/bwt.h
mccortex/libs/bwa/bwt_gen.c
mccortex/libs/bwa/bwt_lite.c
mccortex/libs/bwa/bwt_lite.h
mccortex/libs/bwa/bwtaln.c
mccortex/libs/bwa/bwtaln.h
mccortex/libs/bwa/bwtgap.c
mccortex/libs/bwa/bwtgap.h
mccortex/libs/bwa/bwtindex.c
mccortex/libs/bwa/bwtsw2.h
mccortex/libs/bwa/bwtsw2_aux.c
mccortex/libs/bwa/bwtsw2_chain.c
mccortex/libs/bwa/bwtsw2_core.c
mccortex/libs/bwa/bwtsw2_main.c
mccortex/libs/bwa/bwtsw2_pair.c
mccortex/libs/bwa/example.c
mccortex/libs/bwa/fastmap.c
mccortex/libs/bwa/is.c
mccortex/libs/bwa/kbtree.h
mccortex/libs/bwa/khash.h
mccortex/libs/bwa/kopen.c
mccortex/libs/bwa/kseq.h
mccortex/libs/bwa/ksort.h
mccortex/libs/bwa/kstring.c
mccortex/libs/bwa/kstring.h
mccortex/libs/bwa/ksw.c
mccortex/libs/bwa/ksw.h
mccortex/libs/bwa/kthread.c
mccortex/libs/bwa/kvec.h
mccortex/libs/bwa/main.c
mccortex/libs/bwa/malloc_wrap.c
mccortex/libs/bwa/malloc_wrap.h
mccortex/libs/bwa/maxk.c
mccortex/libs/bwa/pemerge.c
mccortex/libs/bwa/qualfa2fq.pl
mccortex/libs/bwa/utils.c
mccortex/libs/bwa/utils.h
mccortex/libs/bwa/xa2multi.pl
mccortex/libs/bwa/.git/FETCH_HEAD
mccortex/libs/bwa/.git/HEAD
mccortex/libs/bwa/.git/config
mccortex/libs/bwa/.git/description
mccortex/libs/bwa/.git/index
mccortex/libs/bwa/.git/packed-refs
mccortex/libs/bwa/.git/hooks/applypatch-msg.sample
mccortex/libs/bwa/.git/hooks/commit-msg.sample
mccortex/libs/bwa/.git/hooks/post-commit.sample
mccortex/libs/bwa/.git/hooks/post-receive.sample
mccortex/libs/bwa/.git/hooks/post-update.sample
mccortex/libs/bwa/.git/hooks/pre-applypatch.sample
mccortex/libs/bwa/.git/hooks/pre-commit.sample
mccortex/libs/bwa/.git/hooks/pre-rebase.sample
mccortex/libs/bwa/.git/hooks/prepare-commit-msg.sample
mccortex/libs/bwa/.git/hooks/update.sample
mccortex/libs/bwa/.git/info/exclude
mccortex/libs/bwa/.git/logs/HEAD
mccortex/libs/bwa/.git/logs/refs/heads/master
mccortex/libs/bwa/.git/objects/pack/pack-5ad9ffbbdc070b3016359b3689226d31bb51427c.idx
mccortex/libs/bwa/.git/objects/pack/pack-5ad9ffbbdc070b3016359b3689226d31bb51427c.pack
mccortex/libs/bwa/.git/refs/heads/master
mccortex/libs/bwa/.git/refs/remotes/origin/HEAD
mccortex/libs/bwa/bwakit/README.md
mccortex/libs/bwa/bwakit/bwa-postalt.js
mccortex/libs/bwa/bwakit/run-HLA
mccortex/libs/bwa/bwakit/run-bwamem
mccortex/libs/bwa/bwakit/run-gen-ref
mccortex/libs/bwa/bwakit/typeHLA-selctg.js
mccortex/libs/bwa/bwakit/typeHLA.js
mccortex/libs/bwa/bwakit/typeHLA.sh
mccortex/libs/cJSON/LICENSE
mccortex/libs/cJSON/README
mccortex/libs/cJSON/cJSON.c
mccortex/libs/cJSON/cJSON.h
mccortex/libs/cJSON/cJSON.o
mccortex/libs/cJSON/test.c
mccortex/libs/cJSON/tests/test1
mccortex/libs/cJSON/tests/test2
mccortex/libs/cJSON/tests/test3
mccortex/libs/cJSON/tests/test4
mccortex/libs/cJSON/tests/test5
mccortex/libs/carrays/.gitignore
mccortex/libs/carrays/.travis.yml
mccortex/libs/carrays/LICENSE
mccortex/libs/carrays/Makefile
mccortex/libs/carrays/README.md
mccortex/libs/carrays/carrays.c
mccortex/libs/carrays/carrays.h
mccortex/libs/carrays/carrays.o
mccortex/libs/carrays/circ_array.h
mccortex/libs/carrays/runtests
mccortex/libs/carrays/runtests.c
mccortex/libs/carrays/.git/FETCH_HEAD
mccortex/libs/carrays/.git/HEAD
mccortex/libs/carrays/.git/config
mccortex/libs/carrays/.git/description
mccortex/libs/carrays/.git/index
mccortex/libs/carrays/.git/packed-refs
mccortex/libs/carrays/.git/hooks/applypatch-msg.sample
mccortex/libs/carrays/.git/hooks/commit-msg.sample
mccortex/libs/carrays/.git/hooks/post-commit.sample
mccortex/libs/carrays/.git/hooks/post-receive.sample
mccortex/libs/carrays/.git/hooks/post-update.sample
mccortex/libs/carrays/.git/hooks/pre-applypatch.sample
mccortex/libs/carrays/.git/hooks/pre-commit.sample
mccortex/libs/carrays/.git/hooks/pre-rebase.sample
mccortex/libs/carrays/.git/hooks/prepare-commit-msg.sample
mccortex/libs/carrays/.git/hooks/update.sample
mccortex/libs/carrays/.git/info/exclude
mccortex/libs/carrays/.git/logs/HEAD
mccortex/libs/carrays/.git/logs/refs/heads/master
mccortex/libs/carrays/.git/objects/pack/pack-ae4f7074b8dde96220e8e8b6981d0fb4dc28538d.idx
mccortex/libs/carrays/.git/objects/pack/pack-ae4f7074b8dde96220e8e8b6981d0fb4dc28538d.pack
mccortex/libs/carrays/.git/refs/heads/master
mccortex/libs/carrays/.git/refs/remotes/origin/HEAD
mccortex/libs/htslib/.gitattributes
mccortex/libs/htslib/.gitignore
mccortex/libs/htslib/.travis.yml
mccortex/libs/htslib/INSTALL
mccortex/libs/htslib/LICENSE
mccortex/libs/htslib/Makefile
mccortex/libs/htslib/NEWS
mccortex/libs/htslib/README
mccortex/libs/htslib/README.md
mccortex/libs/htslib/bgzf.c
mccortex/libs/htslib/bgzf.o
mccortex/libs/htslib/bgzf.pico
mccortex/libs/htslib/bgzip
mccortex/libs/htslib/bgzip.c
mccortex/libs/htslib/bgzip.o
mccortex/libs/htslib/config.h
mccortex/libs/htslib/config.h.in
mccortex/libs/htslib/config.mk.in
mccortex/libs/htslib/configure.ac
mccortex/libs/htslib/faidx.5
mccortex/libs/htslib/faidx.c
mccortex/libs/htslib/faidx.o
mccortex/libs/htslib/faidx.pico
mccortex/libs/htslib/hfile.c
mccortex/libs/htslib/hfile.o
mccortex/libs/htslib/hfile.pico
mccortex/libs/htslib/hfile_internal.h
mccortex/libs/htslib/hfile_irods.c
mccortex/libs/htslib/hfile_libcurl.c
mccortex/libs/htslib/hfile_net.c
mccortex/libs/htslib/hfile_net.o
mccortex/libs/htslib/hfile_net.pico
mccortex/libs/htslib/hts.c
mccortex/libs/htslib/hts.o
mccortex/libs/htslib/hts.pico
mccortex/libs/htslib/hts_internal.h
mccortex/libs/htslib/htsfile
mccortex/libs/htslib/htsfile.1
mccortex/libs/htslib/htsfile.c
mccortex/libs/htslib/htsfile.o
mccortex/libs/htslib/htslib.mk
mccortex/libs/htslib/htslib.pc.in
mccortex/libs/htslib/htslib_vars.mk
mccortex/libs/htslib/kfunc.c
mccortex/libs/htslib/kfunc.o
mccortex/libs/htslib/kfunc.pico
mccortex/libs/htslib/knetfile.c
mccortex/libs/htslib/knetfile.o
mccortex/libs/htslib/knetfile.pico
mccortex/libs/htslib/kstring.c
mccortex/libs/htslib/kstring.o
mccortex/libs/htslib/kstring.pico
mccortex/libs/htslib/libhts.a
mccortex/libs/htslib/libhts.so
mccortex/libs/htslib/libhts.so.1
mccortex/libs/htslib/md5.c
mccortex/libs/htslib/md5.o
mccortex/libs/htslib/md5.pico
mccortex/libs/htslib/plugin.c
mccortex/libs/htslib/regidx.c
mccortex/libs/htslib/regidx.o
mccortex/libs/htslib/regidx.pico
mccortex/libs/htslib/sam.5
mccortex/libs/htslib/sam.c
mccortex/libs/htslib/sam.o
mccortex/libs/htslib/sam.pico
mccortex/libs/htslib/synced_bcf_reader.c
mccortex/libs/htslib/synced_bcf_reader.o
mccortex/libs/htslib/synced_bcf_reader.pico
mccortex/libs/htslib/tabix
mccortex/libs/htslib/tabix.1
mccortex/libs/htslib/tabix.c
mccortex/libs/htslib/tabix.o
mccortex/libs/htslib/tbx.c
mccortex/libs/htslib/tbx.o
mccortex/libs/htslib/tbx.pico
mccortex/libs/htslib/vcf.5
mccortex/libs/htslib/vcf.c
mccortex/libs/htslib/vcf.o
mccortex/libs/htslib/vcf.pico
mccortex/libs/htslib/vcf_sweep.c
mccortex/libs/htslib/vcf_sweep.o
mccortex/libs/htslib/vcf_sweep.pico
mccortex/libs/htslib/vcfutils.c
mccortex/libs/htslib/vcfutils.o
mccortex/libs/htslib/vcfutils.pico
mccortex/libs/htslib/version.h
mccortex/libs/htslib/.git/FETCH_HEAD
mccortex/libs/htslib/.git/HEAD
mccortex/libs/htslib/.git/config
mccortex/libs/htslib/.git/description
mccortex/libs/htslib/.git/index
mccortex/libs/htslib/.git/packed-refs
mccortex/libs/htslib/.git/hooks/applypatch-msg.sample
mccortex/libs/htslib/.git/hooks/commit-msg.sample
mccortex/libs/htslib/.git/hooks/post-commit.sample
mccortex/libs/htslib/.git/hooks/post-receive.sample
mccortex/libs/htslib/.git/hooks/post-update.sample
mccortex/libs/htslib/.git/hooks/pre-applypatch.sample
mccortex/libs/htslib/.git/hooks/pre-commit.sample
mccortex/libs/htslib/.git/hooks/pre-rebase.sample
mccortex/libs/htslib/.git/hooks/prepare-commit-msg.sample
mccortex/libs/htslib/.git/hooks/update.sample
mccortex/libs/htslib/.git/info/exclude
mccortex/libs/htslib/.git/logs/HEAD
mccortex/libs/htslib/.git/logs/refs/heads/develop
mccortex/libs/htslib/.git/objects/pack/pack-fd4827154cb385b29b8f536fbd7d0a95279c53d2.idx
mccortex/libs/htslib/.git/objects/pack/pack-fd4827154cb385b29b8f536fbd7d0a95279c53d2.pack
mccortex/libs/htslib/.git/refs/heads/develop
mccortex/libs/htslib/.git/refs/remotes/origin/HEAD
mccortex/libs/htslib/cram/cram.h
mccortex/libs/htslib/cram/cram_codecs.c
mccortex/libs/htslib/cram/cram_codecs.h
mccortex/libs/htslib/cram/cram_codecs.o
mccortex/libs/htslib/cram/cram_codecs.pico
mccortex/libs/htslib/cram/cram_decode.c
mccortex/libs/htslib/cram/cram_decode.h
mccortex/libs/htslib/cram/cram_decode.o
mccortex/libs/htslib/cram/cram_decode.pico
mccortex/libs/htslib/cram/cram_encode.c
mccortex/libs/htslib/cram/cram_encode.h
mccortex/libs/htslib/cram/cram_encode.o
mccortex/libs/htslib/cram/cram_encode.pico
mccortex/libs/htslib/cram/cram_external.c
mccortex/libs/htslib/cram/cram_external.o
mccortex/libs/htslib/cram/cram_external.pico
mccortex/libs/htslib/cram/cram_index.c
mccortex/libs/htslib/cram/cram_index.h
mccortex/libs/htslib/cram/cram_index.o
mccortex/libs/htslib/cram/cram_index.pico
mccortex/libs/htslib/cram/cram_io.c
mccortex/libs/htslib/cram/cram_io.h
mccortex/libs/htslib/cram/cram_io.o
mccortex/libs/htslib/cram/cram_io.pico
mccortex/libs/htslib/cram/cram_samtools.c
mccortex/libs/htslib/cram/cram_samtools.h
mccortex/libs/htslib/cram/cram_samtools.o
mccortex/libs/htslib/cram/cram_samtools.pico
mccortex/libs/htslib/cram/cram_stats.c
mccortex/libs/htslib/cram/cram_stats.h
mccortex/libs/htslib/cram/cram_stats.o
mccortex/libs/htslib/cram/cram_stats.pico
mccortex/libs/htslib/cram/cram_structs.h
mccortex/libs/htslib/cram/files.c
mccortex/libs/htslib/cram/files.o
mccortex/libs/htslib/cram/files.pico
mccortex/libs/htslib/cram/mFILE.c
mccortex/libs/htslib/cram/mFILE.h
mccortex/libs/htslib/cram/mFILE.o
mccortex/libs/htslib/cram/mFILE.pico
mccortex/libs/htslib/cram/misc.h
mccortex/libs/htslib/cram/open_trace_file.c
mccortex/libs/htslib/cram/open_trace_file.h
mccortex/libs/htslib/cram/open_trace_file.o
mccortex/libs/htslib/cram/open_trace_file.pico
mccortex/libs/htslib/cram/os.h
mccortex/libs/htslib/cram/pooled_alloc.c
mccortex/libs/htslib/cram/pooled_alloc.h
mccortex/libs/htslib/cram/pooled_alloc.o
mccortex/libs/htslib/cram/pooled_alloc.pico
mccortex/libs/htslib/cram/rANS_byte.h
mccortex/libs/htslib/cram/rANS_static.c
mccortex/libs/htslib/cram/rANS_static.h
mccortex/libs/htslib/cram/rANS_static.o
mccortex/libs/htslib/cram/rANS_static.pico
mccortex/libs/htslib/cram/sam_header.c
mccortex/libs/htslib/cram/sam_header.h
mccortex/libs/htslib/cram/sam_header.o
mccortex/libs/htslib/cram/sam_header.pico
mccortex/libs/htslib/cram/string_alloc.c
mccortex/libs/htslib/cram/string_alloc.h
mccortex/libs/htslib/cram/string_alloc.o
mccortex/libs/htslib/cram/string_alloc.pico
mccortex/libs/htslib/cram/thread_pool.c
mccortex/libs/htslib/cram/thread_pool.h
mccortex/libs/htslib/cram/thread_pool.o
mccortex/libs/htslib/cram/thread_pool.pico
mccortex/libs/htslib/cram/vlen.c
mccortex/libs/htslib/cram/vlen.h
mccortex/libs/htslib/cram/vlen.o
mccortex/libs/htslib/cram/vlen.pico
mccortex/libs/htslib/cram/zfio.c
mccortex/libs/htslib/cram/zfio.h
mccortex/libs/htslib/cram/zfio.o
mccortex/libs/htslib/cram/zfio.pico
mccortex/libs/htslib/htslib/bgzf.h
mccortex/libs/htslib/htslib/cram.h
mccortex/libs/htslib/htslib/faidx.h
mccortex/libs/htslib/htslib/hfile.h
mccortex/libs/htslib/htslib/hts.h
mccortex/libs/htslib/htslib/hts_defs.h
mccortex/libs/htslib/htslib/kbitset.h
mccortex/libs/htslib/htslib/kfunc.h
mccortex/libs/htslib/htslib/khash.h
mccortex/libs/htslib/htslib/khash_str2int.h
mccortex/libs/htslib/htslib/klist.h
mccortex/libs/htslib/htslib/knetfile.h
mccortex/libs/htslib/htslib/kseq.h
mccortex/libs/htslib/htslib/ksort.h
mccortex/libs/htslib/htslib/kstring.h
mccortex/libs/htslib/htslib/regidx.h
mccortex/libs/htslib/htslib/sam.h
mccortex/libs/htslib/htslib/synced_bcf_reader.h
mccortex/libs/htslib/htslib/tbx.h
mccortex/libs/htslib/htslib/vcf.h
mccortex/libs/htslib/htslib/vcf_sweep.h
mccortex/libs/htslib/htslib/vcfutils.h
mccortex/libs/htslib/test/auxf#values.sam
mccortex/libs/htslib/test/auxf.fa
mccortex/libs/htslib/test/auxf.fa.fai
mccortex/libs/htslib/test/c1#bounds.sam
mccortex/libs/htslib/test/c1#clip.sam
mccortex/libs/htslib/test/c1#noseq.sam
mccortex/libs/htslib/test/c1#pad1.sam
mccortex/libs/htslib/test/c1#pad2.sam
mccortex/libs/htslib/test/c1#pad3.sam
mccortex/libs/htslib/test/c1#unknown.sam
mccortex/libs/htslib/test/c1.fa
mccortex/libs/htslib/test/c1.fa.fai
mccortex/libs/htslib/test/c2#pad.sam
mccortex/libs/htslib/test/c2.fa
mccortex/libs/htslib/test/c2.fa.fai
mccortex/libs/htslib/test/ce#1.sam
mccortex/libs/htslib/test/ce#2.sam
mccortex/libs/htslib/test/ce#5.sam
mccortex/libs/htslib/test/ce#5b.sam
mccortex/libs/htslib/test/ce#large_seq.sam
mccortex/libs/htslib/test/ce#supp.sam
mccortex/libs/htslib/test/ce#tag_depadded.sam
mccortex/libs/htslib/test/ce#tag_padded.sam
mccortex/libs/htslib/test/ce#unmap.sam
mccortex/libs/htslib/test/ce#unmap1.sam
mccortex/libs/htslib/test/ce#unmap2.sam
mccortex/libs/htslib/test/ce.fa
mccortex/libs/htslib/test/ce.fa.fai
mccortex/libs/htslib/test/compare_sam.pl
mccortex/libs/htslib/test/cross_validate.sh
mccortex/libs/htslib/test/faidx.fa
mccortex/libs/htslib/test/fieldarith
mccortex/libs/htslib/test/fieldarith.c
mccortex/libs/htslib/test/fieldarith.o
mccortex/libs/htslib/test/fieldarith.sam
mccortex/libs/htslib/test/hfile
mccortex/libs/htslib/test/hfile.c
mccortex/libs/htslib/test/hfile.o
mccortex/libs/htslib/test/sam
mccortex/libs/htslib/test/sam.c
mccortex/libs/htslib/test/sam.o
mccortex/libs/htslib/test/test-regidx
mccortex/libs/htslib/test/test-regidx.c
mccortex/libs/htslib/test/test-regidx.o
mccortex/libs/htslib/test/test-vcf-api
mccortex/libs/htslib/test/test-vcf-api.c
mccortex/libs/htslib/test/test-vcf-api.o
mccortex/libs/htslib/test/test-vcf-api.out
mccortex/libs/htslib/test/test-vcf-hdr-in.vcf
mccortex/libs/htslib/test/test-vcf-hdr.out
mccortex/libs/htslib/test/test-vcf-sweep
mccortex/libs/htslib/test/test-vcf-sweep.c
mccortex/libs/htslib/test/test-vcf-sweep.o
mccortex/libs/htslib/test/test-vcf-sweep.out
mccortex/libs/htslib/test/test.pl
mccortex/libs/htslib/test/test_view
mccortex/libs/htslib/test/test_view.c
mccortex/libs/htslib/test/test_view.o
mccortex/libs/htslib/test/test_view.pl
mccortex/libs/htslib/test/xx#blank.sam
mccortex/libs/htslib/test/xx#large_aux.sam
mccortex/libs/htslib/test/xx#large_aux2.sam
mccortex/libs/htslib/test/xx#minimal.sam
mccortex/libs/htslib/test/xx#pair.sam
mccortex/libs/htslib/test/xx#rg.sam
mccortex/libs/htslib/test/xx#tlen.sam
mccortex/libs/htslib/test/xx#tlen2.sam
mccortex/libs/htslib/test/xx#triplet.sam
mccortex/libs/htslib/test/xx#unsorted.sam
mccortex/libs/htslib/test/xx.fa
mccortex/libs/htslib/test/xx.fa.fai
mccortex/libs/madcrowlib/.gitignore
mccortex/libs/madcrowlib/.travis.yml
mccortex/libs/madcrowlib/LICENSE
mccortex/libs/madcrowlib/Makefile
mccortex/libs/madcrowlib/README.md
mccortex/libs/madcrowlib/madcrow_buffer.h
mccortex/libs/madcrowlib/madcrow_linkedlist.h
mccortex/libs/madcrowlib/madcrow_list.h
mccortex/libs/madcrowlib/madcrowlib.h
mccortex/libs/madcrowlib/run_tests
mccortex/libs/madcrowlib/test.c
mccortex/libs/madcrowlib/.git/FETCH_HEAD
mccortex/libs/madcrowlib/.git/HEAD
mccortex/libs/madcrowlib/.git/config
mccortex/libs/madcrowlib/.git/description
mccortex/libs/madcrowlib/.git/index
mccortex/libs/madcrowlib/.git/packed-refs
mccortex/libs/madcrowlib/.git/hooks/applypatch-msg.sample
mccortex/libs/madcrowlib/.git/hooks/commit-msg.sample
mccortex/libs/madcrowlib/.git/hooks/post-commit.sample
mccortex/libs/madcrowlib/.git/hooks/post-receive.sample
mccortex/libs/madcrowlib/.git/hooks/post-update.sample
mccortex/libs/madcrowlib/.git/hooks/pre-applypatch.sample
mccortex/libs/madcrowlib/.git/hooks/pre-commit.sample
mccortex/libs/madcrowlib/.git/hooks/pre-rebase.sample
mccortex/libs/madcrowlib/.git/hooks/prepare-commit-msg.sample
mccortex/libs/madcrowlib/.git/hooks/update.sample
mccortex/libs/madcrowlib/.git/info/exclude
mccortex/libs/madcrowlib/.git/logs/HEAD
mccortex/libs/madcrowlib/.git/logs/refs/heads/master
mccortex/libs/madcrowlib/.git/objects/pack/pack-ddffef571b29bcfc9360ea8ad9ab168da153d741.idx
mccortex/libs/madcrowlib/.git/objects/pack/pack-ddffef571b29bcfc9360ea8ad9ab168da153d741.pack
mccortex/libs/madcrowlib/.git/refs/heads/master
mccortex/libs/madcrowlib/.git/refs/remotes/origin/HEAD
mccortex/libs/maximal_substrs/Makefile
mccortex/libs/maximal_substrs/maxsubstrs.c
mccortex/libs/maximal_substrs/stream_buffer.h
mccortex/libs/misc/Makefile
mccortex/libs/misc/city.c
mccortex/libs/misc/city.h
mccortex/libs/misc/city.o
mccortex/libs/misc/jenkins.h
mccortex/libs/misc/lookup3.h
mccortex/libs/misc/mem_size.c
mccortex/libs/misc/mem_size.h
mccortex/libs/misc/mem_size.o
mccortex/libs/misc/twang.h
mccortex/libs/msg-pool/.gitignore
mccortex/libs/msg-pool/Makefile
mccortex/libs/msg-pool/README.md
mccortex/libs/msg-pool/msgpool.h
mccortex/libs/msg-pool/test.c
mccortex/libs/msg-pool/test_msgpool
mccortex/libs/msg-pool/thread_pause.h
mccortex/libs/msg-pool/.git/FETCH_HEAD
mccortex/libs/msg-pool/.git/HEAD
mccortex/libs/msg-pool/.git/config
mccortex/libs/msg-pool/.git/description
mccortex/libs/msg-pool/.git/index
mccortex/libs/msg-pool/.git/packed-refs
mccortex/libs/msg-pool/.git/hooks/applypatch-msg.sample
mccortex/libs/msg-pool/.git/hooks/commit-msg.sample
mccortex/libs/msg-pool/.git/hooks/post-commit.sample
mccortex/libs/msg-pool/.git/hooks/post-receive.sample
mccortex/libs/msg-pool/.git/hooks/post-update.sample
mccortex/libs/msg-pool/.git/hooks/pre-applypatch.sample
mccortex/libs/msg-pool/.git/hooks/pre-commit.sample
mccortex/libs/msg-pool/.git/hooks/pre-rebase.sample
mccortex/libs/msg-pool/.git/hooks/prepare-commit-msg.sample
mccortex/libs/msg-pool/.git/hooks/update.sample
mccortex/libs/msg-pool/.git/info/exclude
mccortex/libs/msg-pool/.git/logs/HEAD
mccortex/libs/msg-pool/.git/logs/refs/heads/master
mccortex/libs/msg-pool/.git/objects/02/7bc26eb0133306316aa244afbd6a928571715c
mccortex/libs/msg-pool/.git/objects/04/544418d5389fde8edffe8cc581a5fa4b494606
mccortex/libs/msg-pool/.git/objects/07/b77cb37a75b6f68f637716cb7871430b90de02
mccortex/libs/msg-pool/.git/objects/0f/7bd28eafed945fea9c74450620f7f2a8dd21e8
mccortex/libs/msg-pool/.git/objects/14/b17749acc142599c4211c0516eee0e32aa68de
mccortex/libs/msg-pool/.git/objects/18/31c63039eae5974f3c8c8af65e4dd99f14f2a2
mccortex/libs/msg-pool/.git/objects/18/7fdd68d8af5596885fa031c252d9bc5093f777
mccortex/libs/msg-pool/.git/objects/18/f0c991f01defdf0e8bced605818987e4132bde
mccortex/libs/msg-pool/.git/objects/19/843443a2f5471984f822fde53c3942ef747faf
mccortex/libs/msg-pool/.git/objects/1a/b6019f0d8e713796c3b64a307600ccd57d3f8b
mccortex/libs/msg-pool/.git/objects/1b/39264e05f5e88089e2989942267083e8595831
mccortex/libs/msg-pool/.git/objects/1e/cc976785ef2d841c897d0ca685ddbd68f914bc
mccortex/libs/msg-pool/.git/objects/20/ad8fd26c49f13e76417247d515b0c48ac6592e
mccortex/libs/msg-pool/.git/objects/22/2b28829f73327a3dea143c8f3562425cbc1f64
mccortex/libs/msg-pool/.git/objects/23/f89f1e273c644ec550528a83ef7e6725afec92
mccortex/libs/msg-pool/.git/objects/2c/7fa1486e2ce8f83c4d8fc02899a81934963b16
mccortex/libs/msg-pool/.git/objects/2f/1cbfd501fcf1636fcabf20332147f959acda1b
mccortex/libs/msg-pool/.git/objects/30/630fc7402e857c9a6ffa806f81cfcf7a8531da
mccortex/libs/msg-pool/.git/objects/33/3c834d14da54eb7de3ceaf8b9a234f444c4f72
mccortex/libs/msg-pool/.git/objects/34/9a52fbcb908567849838b8a4ce7c0fe6192f08
mccortex/libs/msg-pool/.git/objects/39/e13e800fa2edbf0bb7f42b2f98b5b09ca6c548
mccortex/libs/msg-pool/.git/objects/3c/766d4051b7f348e05b8a6dd717a763a35da7ca
mccortex/libs/msg-pool/.git/objects/3c/c58c32849cb0f10060982d06fd66d77058da7e
mccortex/libs/msg-pool/.git/objects/3e/03205d1291be7eb8d5bcc91ad31dcb8a27917d
mccortex/libs/msg-pool/.git/objects/42/c3628de77d3f587bbc3fdf5b7b16664c31de6a
mccortex/libs/msg-pool/.git/objects/49/f1409918ae18dcd2f6dcf16d697feb16c9b71a
mccortex/libs/msg-pool/.git/objects/4c/1d4c705cdc268be1be8d3784e42f162906adde
mccortex/libs/msg-pool/.git/objects/51/19156d4d016e76d596c19808f6cb3f28e974ec
mccortex/libs/msg-pool/.git/objects/52/fcfc0772af2419486db3206cfa7cdfd674f18e
mccortex/libs/msg-pool/.git/objects/56/d14c4f11c4f1d7a8d30f6027aa24b48cbae966
mccortex/libs/msg-pool/.git/objects/57/4b70cbf16126ad28d9676b6f66e75c81d566a3
mccortex/libs/msg-pool/.git/objects/58/0f9c1f55c1bdaa0b6dc81391be4db6bdc4ae73
mccortex/libs/msg-pool/.git/objects/5b/ac876975189512577d0549d132d181fc532dfd
mccortex/libs/msg-pool/.git/objects/5f/08bc1eb340fc6b671f8e567ac9887d5b95e5a5
mccortex/libs/msg-pool/.git/objects/62/1f0ab07bed8b37e3f3cbb16167ee5c79555b89
mccortex/libs/msg-pool/.git/objects/6d/c47c656f3abb1c0fb0b1522eb708db2bf7db3f
mccortex/libs/msg-pool/.git/objects/6d/cd677542f2fbdc3cee9d56028d9665429ba3de
mccortex/libs/msg-pool/.git/objects/6e/b722124c31e4bcd44947d2894dd7552a76c0a7
mccortex/libs/msg-pool/.git/objects/70/17b3b32307645d0aad3b332c1fece51cccb49e
mccortex/libs/msg-pool/.git/objects/72/8ac9e3308c81bab24bdf34b4f621793242e6d7
mccortex/libs/msg-pool/.git/objects/72/f6535a6ae90a2205d695ac7a55f2527b522f8b
mccortex/libs/msg-pool/.git/objects/74/b880bf3e3e62a56474542cd23537420008ff3f
mccortex/libs/msg-pool/.git/objects/74/c731f8cf566c105dcde5c549aeee530bf1bd50
mccortex/libs/msg-pool/.git/objects/75/db9c1d515c41c667063645e9730096f0b41a46
mccortex/libs/msg-pool/.git/objects/7c/671f1dd50a76508e2032761bd272b61507c9e3
mccortex/libs/msg-pool/.git/objects/7c/b9214e91ee4d18331a80dc5b6705349bc8e259
mccortex/libs/msg-pool/.git/objects/7e/f9dac28148275263db8971474f5226b132ff82
mccortex/libs/msg-pool/.git/objects/85/0201e0212150137bb2bbfaee63fab35cdd29d2
mccortex/libs/msg-pool/.git/objects/90/e43bf5b962a5ea1ad86c4e9a325fb116fbd19c
mccortex/libs/msg-pool/.git/objects/94/20957fb312c46770592ceb831e9997aeca9caa
mccortex/libs/msg-pool/.git/objects/9c/01de32380f375e1332d0f350e8eb95588b5bd4
mccortex/libs/msg-pool/.git/objects/a4/edb1246ccec5a186c0831b8dcb98e9182a6379
mccortex/libs/msg-pool/.git/objects/a5/461941dc221aaf882e0c1b4213f0f1c6bbffea
mccortex/libs/msg-pool/.git/objects/a7/8eadffae03aa6d1dec93915742d76af99055fc
mccortex/libs/msg-pool/.git/objects/a7/94199fc8fc6e435d8b0b5431b0329f7d9db9e4
mccortex/libs/msg-pool/.git/objects/a8/46b3d96944a3297e89c2bdb3e087b8613fcba1
mccortex/libs/msg-pool/.git/objects/aa/b0a49085774d4c5136a70ca30779eda2b4d590
mccortex/libs/msg-pool/.git/objects/ab/513f15a8552643c092b311006386ad846303d1
mccortex/libs/msg-pool/.git/objects/ac/444f707e49153de1d136a61c18e800f7095392
mccortex/libs/msg-pool/.git/objects/af/562f3517ca98b784f3ac5058501e80e0f795c8
mccortex/libs/msg-pool/.git/objects/af/7e834795bf3c756675bab06b6f26f270d8c466
mccortex/libs/msg-pool/.git/objects/b1/9534521189621d29633cabbebacce9181cfd9d
mccortex/libs/msg-pool/.git/objects/b3/382725fa1653d857ad13bc35b81ad8c8fe138a
mccortex/libs/msg-pool/.git/objects/b3/8764eaf86fb39f2fa14caa2088a3fa517424d8
mccortex/libs/msg-pool/.git/objects/b8/d59e356234a8c4761416cdd48deced6ee7b647
mccortex/libs/msg-pool/.git/objects/b9/e8baba2e30cae5e8b74c939abacb7cdb67523f
mccortex/libs/msg-pool/.git/objects/ba/b0777d12b158153ae711428174c2202b65fcbb
mccortex/libs/msg-pool/.git/objects/bb/b5452373c821712e584fc2bb974a57fb17dc1e
mccortex/libs/msg-pool/.git/objects/be/184d6cbe7485791035255a858c0a5709c2a144
mccortex/libs/msg-pool/.git/objects/c1/39ee3fc1ce21b808385a9dba0be14f407e429c
mccortex/libs/msg-pool/.git/objects/c4/19d4ef27270cb5604508f5df784cee8879cfad
mccortex/libs/msg-pool/.git/objects/c5/ae157f30100babef3f4bca0a3fdd0580643c1a
mccortex/libs/msg-pool/.git/objects/ca/e4823fbb17130653ffa9039ffc8f4722286bba
mccortex/libs/msg-pool/.git/objects/cd/ce91e435a43ff6d11075b698d327056de55e7a
mccortex/libs/msg-pool/.git/objects/ce/364129782cf6e5a81f05c2cde3c50e2f33f804
mccortex/libs/msg-pool/.git/objects/d1/8b11ea28a56117d3e4361d1730e3b2cd5e91f8
mccortex/libs/msg-pool/.git/objects/d2/39f831775fb02f591253af2305606a7ca5f436
mccortex/libs/msg-pool/.git/objects/d8/46e22e7d6becec4b27eede43f1ef3c855dc039
mccortex/libs/msg-pool/.git/objects/d8/ca907932a18effb947b13fbdfa41edb7c08bfb
mccortex/libs/msg-pool/.git/objects/da/c15be3939a0d6cd774fe40ac89b01bf63f045a
mccortex/libs/msg-pool/.git/objects/db/80460ad2a92f1c9c9aeaad3fb528872ea05f0e
mccortex/libs/msg-pool/.git/objects/dc/a51fa6d9ea10e4fb7ca8d6e8553679617cebc8
mccortex/libs/msg-pool/.git/objects/e3/4fcd604c1fa89a48293c0613d3ecb7b03d4fd7
mccortex/libs/msg-pool/.git/objects/e5/baf00ec1de16079753f3200d7c0a81830b3802
mccortex/libs/msg-pool/.git/objects/ec/a5643f3286fd34879a8971ec5a56f2c7876d18
mccortex/libs/msg-pool/.git/objects/ee/2a930dbd0de6b05e80012970b2498ba9555c55
mccortex/libs/msg-pool/.git/objects/f0/4417dcf7a2b6ee020a602eecffebc877f3493e
mccortex/libs/msg-pool/.git/objects/f1/2938bc5fd14ab836640cf0a09f2f2897e98cbd
mccortex/libs/msg-pool/.git/objects/f1/752c65a4d00146d18027e052b2ff0458ac93d9
mccortex/libs/msg-pool/.git/objects/f1/b7891746522f36e937fa3fda941d9e725866d8
mccortex/libs/msg-pool/.git/objects/f2/45987941f2962eb5938871bedd39590f43004a
mccortex/libs/msg-pool/.git/objects/f8/bb66b8332605bbe1cd4e9e4fbcf2308c13a014
mccortex/libs/msg-pool/.git/objects/fc/af9f0222c71625c05e5d5b6e6db8375e96bae5
mccortex/libs/msg-pool/.git/objects/ff/424621b090fb1d8694aa77557490b5910563f6
mccortex/libs/msg-pool/.git/objects/ff/fbe1cef38b94f1332a7d0a71cb1f8d86808d0d
mccortex/libs/msg-pool/.git/refs/heads/master
mccortex/libs/msg-pool/.git/refs/remotes/origin/HEAD
mccortex/libs/readsim/.gitignore
mccortex/libs/readsim/Makefile
mccortex/libs/readsim/README.md
mccortex/libs/readsim/plot.R
mccortex/libs/readsim/readsim.c
mccortex/libs/readsim/seq_file.h
mccortex/libs/readsim/stream_buffer.h
mccortex/libs/readsim/.git/FETCH_HEAD
mccortex/libs/readsim/.git/HEAD
mccortex/libs/readsim/.git/config
mccortex/libs/readsim/.git/description
mccortex/libs/readsim/.git/index
mccortex/libs/readsim/.git/packed-refs
mccortex/libs/readsim/.git/hooks/applypatch-msg.sample
mccortex/libs/readsim/.git/hooks/commit-msg.sample
mccortex/libs/readsim/.git/hooks/post-commit.sample
mccortex/libs/readsim/.git/hooks/post-receive.sample
mccortex/libs/readsim/.git/hooks/post-update.sample
mccortex/libs/readsim/.git/hooks/pre-applypatch.sample
mccortex/libs/readsim/.git/hooks/pre-commit.sample
mccortex/libs/readsim/.git/hooks/pre-rebase.sample
mccortex/libs/readsim/.git/hooks/prepare-commit-msg.sample
mccortex/libs/readsim/.git/hooks/update.sample
mccortex/libs/readsim/.git/info/exclude
mccortex/libs/readsim/.git/logs/HEAD
mccortex/libs/readsim/.git/logs/refs/heads/master
mccortex/libs/readsim/.git/objects/pack/pack-c2fdeeb1e51ee08380ae6bb0f20318f29c3e09cc.idx
mccortex/libs/readsim/.git/objects/pack/pack-c2fdeeb1e51ee08380ae6bb0f20318f29c3e09cc.pack
mccortex/libs/readsim/.git/refs/heads/master
mccortex/libs/readsim/.git/refs/remotes/origin/HEAD
mccortex/libs/samtools/.gitattributes
mccortex/libs/samtools/.gitignore
mccortex/libs/samtools/.travis.yml
mccortex/libs/samtools/AUTHORS
mccortex/libs/samtools/ChangeLog.old
mccortex/libs/samtools/INSTALL
mccortex/libs/samtools/LICENSE
mccortex/libs/samtools/Makefile
mccortex/libs/samtools/Makefile.mingw
mccortex/libs/samtools/NEWS
mccortex/libs/samtools/README
mccortex/libs/samtools/README.md
mccortex/libs/samtools/bam.c
mccortex/libs/samtools/bam.h
mccortex/libs/samtools/bam2bcf.c
mccortex/libs/samtools/bam2bcf.h
mccortex/libs/samtools/bam2bcf_indel.c
mccortex/libs/samtools/bam2depth.c
mccortex/libs/samtools/bam_addrprg.c
mccortex/libs/samtools/bam_aux.c
mccortex/libs/samtools/bam_cat.c
mccortex/libs/samtools/bam_color.c
mccortex/libs/samtools/bam_endian.h
mccortex/libs/samtools/bam_flags.c
mccortex/libs/samtools/bam_import.c
mccortex/libs/samtools/bam_index.c
mccortex/libs/samtools/bam_lpileup.c
mccortex/libs/samtools/bam_lpileup.h
mccortex/libs/samtools/bam_mate.c
mccortex/libs/samtools/bam_md.c
mccortex/libs/samtools/bam_plbuf.c
mccortex/libs/samtools/bam_plbuf.h
mccortex/libs/samtools/bam_plcmd.c
mccortex/libs/samtools/bam_quickcheck.c
mccortex/libs/samtools/bam_reheader.c
mccortex/libs/samtools/bam_rmdup.c
mccortex/libs/samtools/bam_rmdupse.c
mccortex/libs/samtools/bam_sort.c
mccortex/libs/samtools/bam_split.c
mccortex/libs/samtools/bam_stat.c
mccortex/libs/samtools/bam_tview.c
mccortex/libs/samtools/bam_tview.h
mccortex/libs/samtools/bam_tview_curses.c
mccortex/libs/samtools/bam_tview_html.c
mccortex/libs/samtools/bamshuf.c
mccortex/libs/samtools/bamtk.c
mccortex/libs/samtools/bedcov.c
mccortex/libs/samtools/bedidx.c
mccortex/libs/samtools/cut_target.c
mccortex/libs/samtools/dict.c
mccortex/libs/samtools/errmod.c
mccortex/libs/samtools/errmod.h
mccortex/libs/samtools/faidx.c
mccortex/libs/samtools/kprobaln.c
mccortex/libs/samtools/kprobaln.h
mccortex/libs/samtools/padding.c
mccortex/libs/samtools/phase.c
mccortex/libs/samtools/sam.c
mccortex/libs/samtools/sam.h
mccortex/libs/samtools/sam_header.c
mccortex/libs/samtools/sam_header.h
mccortex/libs/samtools/sam_opts.c
mccortex/libs/samtools/sam_opts.h
mccortex/libs/samtools/sam_view.c
mccortex/libs/samtools/sample.c
mccortex/libs/samtools/sample.h
mccortex/libs/samtools/samtools.1
mccortex/libs/samtools/samtools.h
mccortex/libs/samtools/stats.c
mccortex/libs/samtools/stats_isize.c
mccortex/libs/samtools/stats_isize.h
mccortex/libs/samtools/.git/FETCH_HEAD
mccortex/libs/samtools/.git/HEAD
mccortex/libs/samtools/.git/config
mccortex/libs/samtools/.git/description
mccortex/libs/samtools/.git/index
mccortex/libs/samtools/.git/packed-refs
mccortex/libs/samtools/.git/hooks/applypatch-msg.sample
mccortex/libs/samtools/.git/hooks/commit-msg.sample
mccortex/libs/samtools/.git/hooks/post-commit.sample
mccortex/libs/samtools/.git/hooks/post-receive.sample
mccortex/libs/samtools/.git/hooks/post-update.sample
mccortex/libs/samtools/.git/hooks/pre-applypatch.sample
mccortex/libs/samtools/.git/hooks/pre-commit.sample
mccortex/libs/samtools/.git/hooks/pre-rebase.sample
mccortex/libs/samtools/.git/hooks/prepare-commit-msg.sample
mccortex/libs/samtools/.git/hooks/update.sample
mccortex/libs/samtools/.git/info/exclude
mccortex/libs/samtools/.git/logs/HEAD
mccortex/libs/samtools/.git/logs/refs/heads/develop
mccortex/libs/samtools/.git/objects/pack/pack-162c886e4fb2e25b310baf2f17082ee0560d0d5a.idx
mccortex/libs/samtools/.git/objects/pack/pack-162c886e4fb2e25b310baf2f17082ee0560d0d5a.pack
mccortex/libs/samtools/.git/refs/heads/develop
mccortex/libs/samtools/.git/refs/remotes/origin/HEAD
mccortex/libs/samtools/.travis/clone
mccortex/libs/samtools/examples/.gitignore
mccortex/libs/samtools/examples/00README.txt
mccortex/libs/samtools/examples/ex1.fa
mccortex/libs/samtools/examples/ex1.sam.gz
mccortex/libs/samtools/examples/toy.fa
mccortex/libs/samtools/examples/toy.sam
mccortex/libs/samtools/misc/HmmGlocal.java
mccortex/libs/samtools/misc/ace2sam.c
mccortex/libs/samtools/misc/blast2sam.pl
mccortex/libs/samtools/misc/bowtie2sam.pl
mccortex/libs/samtools/misc/export2sam.pl
mccortex/libs/samtools/misc/interpolate_sam.pl
mccortex/libs/samtools/misc/maq2sam.c
mccortex/libs/samtools/misc/md5fa.c
mccortex/libs/samtools/misc/md5sum-lite.c
mccortex/libs/samtools/misc/novo2sam.pl
mccortex/libs/samtools/misc/plot-bamstats
mccortex/libs/samtools/misc/psl2sam.pl
mccortex/libs/samtools/misc/r2plot.lua
mccortex/libs/samtools/misc/sam2vcf.pl
mccortex/libs/samtools/misc/samtools.pl
mccortex/libs/samtools/misc/seq_cache_populate.pl
mccortex/libs/samtools/misc/soap2sam.pl
mccortex/libs/samtools/misc/varfilter.py
mccortex/libs/samtools/misc/vcfutils.lua
mccortex/libs/samtools/misc/wgsim.1
mccortex/libs/samtools/misc/wgsim.c
mccortex/libs/samtools/misc/wgsim_eval.pl
mccortex/libs/samtools/misc/zoom2sam.pl
mccortex/libs/samtools/test/test.c
mccortex/libs/samtools/test/test.h
mccortex/libs/samtools/test/test.pl
mccortex/libs/samtools/test/vcf-miniview.c
mccortex/libs/samtools/test/addrprg/1_fixup.sam
mccortex/libs/samtools/test/addrprg/1_fixup.sam.expected
mccortex/libs/samtools/test/addrprg/1_fixup.sam.expected.err
mccortex/libs/samtools/test/addrprg/2_fixup_orphan.sam
mccortex/libs/samtools/test/addrprg/2_fixup_orphan.sam.expected
mccortex/libs/samtools/test/addrprg/2_fixup_orphan.sam.expected.err
mccortex/libs/samtools/test/addrprg/3_fixup.sam.expected
mccortex/libs/samtools/test/addrprg/3_fixup.sam.expected.err
mccortex/libs/samtools/test/addrprg/4_fixup_norg.sam
mccortex/libs/samtools/test/addrprg/4_fixup_norg.sam.expected
mccortex/libs/samtools/test/addrprg/4_fixup_norg.sam.expected.err
mccortex/libs/samtools/test/bam2fq/1.1.fq.expected
mccortex/libs/samtools/test/bam2fq/1.2.fq.expected
mccortex/libs/samtools/test/bam2fq/1.stdout.expected
mccortex/libs/samtools/test/bam2fq/2.1.fq.expected
mccortex/libs/samtools/test/bam2fq/2.2.fq.expected
mccortex/libs/samtools/test/bam2fq/2.s.fq.expected
mccortex/libs/samtools/test/bam2fq/2.stdout.expected
mccortex/libs/samtools/test/bam2fq/3.1.fq.expected
mccortex/libs/samtools/test/bam2fq/3.2.fq.expected
mccortex/libs/samtools/test/bam2fq/3.s.fq.expected
mccortex/libs/samtools/test/bam2fq/3.stdout.expected
mccortex/libs/samtools/test/bam2fq/4.1.fq.expected
mccortex/libs/samtools/test/bam2fq/4.2.fq.expected
mccortex/libs/samtools/test/bam2fq/4.s.fq.expected
mccortex/libs/samtools/test/bam2fq/4.stdout.expected
mccortex/libs/samtools/test/dat/.gitignore
mccortex/libs/samtools/test/dat/bam2fq.001.sam
mccortex/libs/samtools/test/dat/bam2fq.002.sam
mccortex/libs/samtools/test/dat/bam2fq.003.sam
mccortex/libs/samtools/test/dat/cat.hdr
mccortex/libs/samtools/test/dat/depad.001.fa
mccortex/libs/samtools/test/dat/depad.001.fa.fai
mccortex/libs/samtools/test/dat/depad.001p.sam
mccortex/libs/samtools/test/dat/depad.001u.sam
mccortex/libs/samtools/test/dat/dict.fa
mccortex/libs/samtools/test/dat/dict.out
mccortex/libs/samtools/test/dat/empty.expected
mccortex/libs/samtools/test/dat/large_chrom.out
mccortex/libs/samtools/test/dat/large_chrom.sam
mccortex/libs/samtools/test/dat/large_chrom_bai_index.err
mccortex/libs/samtools/test/dat/mpileup.1.sam
mccortex/libs/samtools/test/dat/mpileup.2.sam
mccortex/libs/samtools/test/dat/mpileup.3.sam
mccortex/libs/samtools/test/dat/mpileup.err.1
mccortex/libs/samtools/test/dat/mpileup.out.1
mccortex/libs/samtools/test/dat/mpileup.out.2
mccortex/libs/samtools/test/dat/mpileup.out.3
mccortex/libs/samtools/test/dat/mpileup.out.4
mccortex/libs/samtools/test/dat/mpileup.ref.fa
mccortex/libs/samtools/test/dat/mpileup.ref.fa.fai
mccortex/libs/samtools/test/dat/test_input_1_a.bam
mccortex/libs/samtools/test/dat/test_input_1_a.bam.bai.expected
mccortex/libs/samtools/test/dat/test_input_1_a.sam
mccortex/libs/samtools/test/dat/test_input_1_a_regex.sam
mccortex/libs/samtools/test/dat/test_input_1_b.bam
mccortex/libs/samtools/test/dat/test_input_1_b.sam
mccortex/libs/samtools/test/dat/test_input_1_b_regex.sam
mccortex/libs/samtools/test/dat/test_input_1_c.bam
mccortex/libs/samtools/test/dat/test_input_1_c.sam
mccortex/libs/samtools/test/dat/view.001.01.bed
mccortex/libs/samtools/test/dat/view.001.02.bed
mccortex/libs/samtools/test/dat/view.001.fa
mccortex/libs/samtools/test/dat/view.001.fa.fai
mccortex/libs/samtools/test/dat/view.001.sam
mccortex/libs/samtools/test/dat/view.002.01.bed
mccortex/libs/samtools/test/dat/view.002.02.bed
mccortex/libs/samtools/test/dat/view.002.fa
mccortex/libs/samtools/test/dat/view.002.fa.fai
mccortex/libs/samtools/test/dat/view.002.sam
mccortex/libs/samtools/test/dat/view.003.expected.sam
mccortex/libs/samtools/test/dat/view.003.sam
mccortex/libs/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
mccortex/libs/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
mccortex/libs/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
mccortex/libs/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
mccortex/libs/samtools/test/fixmate/1_coord_sort.sam
mccortex/libs/samtools/test/fixmate/1_coord_sort.sam.expected
mccortex/libs/samtools/test/fixmate/1_coord_sort.sam.expected.err
mccortex/libs/samtools/test/fixmate/2_isize_overflow.sam
mccortex/libs/samtools/test/fixmate/2_isize_overflow.sam.expected
mccortex/libs/samtools/test/fixmate/3_reverse_read_pp_lt.sam
mccortex/libs/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected
mccortex/libs/samtools/test/fixmate/4_reverse_read_pp_equal.sam
mccortex/libs/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected
mccortex/libs/samtools/test/fixmate/5_ct.sam
mccortex/libs/samtools/test/fixmate/5_ct.sam.expected
mccortex/libs/samtools/test/fixmate/6_ct_replace.sam
mccortex/libs/samtools/test/fixmate/6_ct_replace.sam.expected
mccortex/libs/samtools/test/idxstats/test_input_1_a.bam.expected
mccortex/libs/samtools/test/idxstats/test_input_1_a.bam.expected.err
mccortex/libs/samtools/test/merge/.gitignore
mccortex/libs/samtools/test/merge/2.merge.expected.bam
mccortex/libs/samtools/test/merge/3.merge.expected.bam
mccortex/libs/samtools/test/merge/3.merge.expected.err
mccortex/libs/samtools/test/merge/4.merge.expected.bam
mccortex/libs/samtools/test/merge/5.merge.expected.bam
mccortex/libs/samtools/test/merge/5.merge.expected.sam
mccortex/libs/samtools/test/merge/6.merge.expected.bam
mccortex/libs/samtools/test/merge/7.merge.expected.bam
mccortex/libs/samtools/test/merge/test_3.fofn
mccortex/libs/samtools/test/merge/test_bam_translate.c
mccortex/libs/samtools/test/merge/test_header.sam
mccortex/libs/samtools/test/merge/test_rtrans_build.c
mccortex/libs/samtools/test/merge/test_trans_tbl_init.c
mccortex/libs/samtools/test/mpileup/.gitignore
mccortex/libs/samtools/test/mpileup/1read.bam
mccortex/libs/samtools/test/mpileup/1read.sam
mccortex/libs/samtools/test/mpileup/anomalous.sam
mccortex/libs/samtools/test/mpileup/c1#ID.bam
mccortex/libs/samtools/test/mpileup/c1#ID2.bam
mccortex/libs/samtools/test/mpileup/c1#clip.bam
mccortex/libs/samtools/test/mpileup/c1#pad1.bam
mccortex/libs/samtools/test/mpileup/c1#pad2.bam
mccortex/libs/samtools/test/mpileup/c1#pad3.bam
mccortex/libs/samtools/test/mpileup/c1.fa
mccortex/libs/samtools/test/mpileup/c1.fa.fai
mccortex/libs/samtools/test/mpileup/ce#5b.bam
mccortex/libs/samtools/test/mpileup/ce#5b.bam.bai
mccortex/libs/samtools/test/mpileup/ce#5b.cram
mccortex/libs/samtools/test/mpileup/ce#5b.cram.crai
mccortex/libs/samtools/test/mpileup/ce#5b.sam
mccortex/libs/samtools/test/mpileup/ce#large_seq.bam
mccortex/libs/samtools/test/mpileup/ce#unmap.bam
mccortex/libs/samtools/test/mpileup/ce#unmap1.bam
mccortex/libs/samtools/test/mpileup/ce#unmap2.bam
mccortex/libs/samtools/test/mpileup/ce.fa
mccortex/libs/samtools/test/mpileup/ce.fa.fai
mccortex/libs/samtools/test/mpileup/deep.sam
mccortex/libs/samtools/test/mpileup/depth.reg
mccortex/libs/samtools/test/mpileup/indels.sam
mccortex/libs/samtools/test/mpileup/mpileup-E.bam
mccortex/libs/samtools/test/mpileup/mpileup.1.bam
mccortex/libs/samtools/test/mpileup/mpileup.1.bam.bai
mccortex/libs/samtools/test/mpileup/mpileup.2.bam
mccortex/libs/samtools/test/mpileup/mpileup.3.bam
mccortex/libs/samtools/test/mpileup/mpileup.ref.fa
mccortex/libs/samtools/test/mpileup/mpileup.ref.fa.fai
mccortex/libs/samtools/test/mpileup/mpileup.reg
mccortex/libs/samtools/test/mpileup/overlap50.sam
mccortex/libs/samtools/test/mpileup/overlapIllumina.bam
mccortex/libs/samtools/test/mpileup/regions
mccortex/libs/samtools/test/mpileup/regression.sh
mccortex/libs/samtools/test/mpileup/xx#depth1.sam
mccortex/libs/samtools/test/mpileup/xx#depth2.sam
mccortex/libs/samtools/test/mpileup/xx#minimal.bam
mccortex/libs/samtools/test/mpileup/xx#triplet.bam
mccortex/libs/samtools/test/mpileup/xx.bed
mccortex/libs/samtools/test/mpileup/xx.bed2
mccortex/libs/samtools/test/mpileup/xx.fa
mccortex/libs/samtools/test/mpileup/xx.fa.fai
mccortex/libs/samtools/test/mpileup/expected/1.out.f3-6.gz
mccortex/libs/samtools/test/mpileup/expected/10.out
mccortex/libs/samtools/test/mpileup/expected/11.out
mccortex/libs/samtools/test/mpileup/expected/12.out
mccortex/libs/samtools/test/mpileup/expected/13.out
mccortex/libs/samtools/test/mpileup/expected/14.out
mccortex/libs/samtools/test/mpileup/expected/15.out
mccortex/libs/samtools/test/mpileup/expected/16.out
mccortex/libs/samtools/test/mpileup/expected/17.out
mccortex/libs/samtools/test/mpileup/expected/18.out
mccortex/libs/samtools/test/mpileup/expected/19.out
mccortex/libs/samtools/test/mpileup/expected/2.out
mccortex/libs/samtools/test/mpileup/expected/20.out
mccortex/libs/samtools/test/mpileup/expected/21.out
mccortex/libs/samtools/test/mpileup/expected/22.out
mccortex/libs/samtools/test/mpileup/expected/23.out
mccortex/libs/samtools/test/mpileup/expected/24.out
mccortex/libs/samtools/test/mpileup/expected/25.out
mccortex/libs/samtools/test/mpileup/expected/26.out
mccortex/libs/samtools/test/mpileup/expected/27.out
mccortex/libs/samtools/test/mpileup/expected/28.out
mccortex/libs/samtools/test/mpileup/expected/29.out
mccortex/libs/samtools/test/mpileup/expected/3.out
mccortex/libs/samtools/test/mpileup/expected/30.out
mccortex/libs/samtools/test/mpileup/expected/31.out
mccortex/libs/samtools/test/mpileup/expected/32.out
mccortex/libs/samtools/test/mpileup/expected/33.out
mccortex/libs/samtools/test/mpileup/expected/34.out
mccortex/libs/samtools/test/mpileup/expected/35.out
mccortex/libs/samtools/test/mpileup/expected/37.out
mccortex/libs/samtools/test/mpileup/expected/38.out
mccortex/libs/samtools/test/mpileup/expected/39.out
mccortex/libs/samtools/test/mpileup/expected/4.out
mccortex/libs/samtools/test/mpileup/expected/40.out
mccortex/libs/samtools/test/mpileup/expected/41.out
mccortex/libs/samtools/test/mpileup/expected/42.out
mccortex/libs/samtools/test/mpileup/expected/43.out
mccortex/libs/samtools/test/mpileup/expected/44.out
mccortex/libs/samtools/test/mpileup/expected/45.out
mccortex/libs/samtools/test/mpileup/expected/46.out
mccortex/libs/samtools/test/mpileup/expected/47.out
mccortex/libs/samtools/test/mpileup/expected/48.out
mccortex/libs/samtools/test/mpileup/expected/49.out
mccortex/libs/samtools/test/mpileup/expected/5.out
mccortex/libs/samtools/test/mpileup/expected/50.out
mccortex/libs/samtools/test/mpileup/expected/51.out
mccortex/libs/samtools/test/mpileup/expected/52.out
mccortex/libs/samtools/test/mpileup/expected/53.out
mccortex/libs/samtools/test/mpileup/expected/54.out
mccortex/libs/samtools/test/mpileup/expected/55.out
mccortex/libs/samtools/test/mpileup/expected/56.out
mccortex/libs/samtools/test/mpileup/expected/57.out
mccortex/libs/samtools/test/mpileup/expected/58.out
mccortex/libs/samtools/test/mpileup/expected/59.out
mccortex/libs/samtools/test/mpileup/expected/6.out
mccortex/libs/samtools/test/mpileup/expected/60.out
mccortex/libs/samtools/test/mpileup/expected/61.out
mccortex/libs/samtools/test/mpileup/expected/62.out
mccortex/libs/samtools/test/mpileup/expected/63.out
mccortex/libs/samtools/test/mpileup/expected/64.out
mccortex/libs/samtools/test/mpileup/expected/65.out
mccortex/libs/samtools/test/mpileup/expected/66.out
mccortex/libs/samtools/test/mpileup/expected/67.out
mccortex/libs/samtools/test/mpileup/expected/68.out
mccortex/libs/samtools/test/mpileup/expected/69.out
mccortex/libs/samtools/test/mpileup/expected/7.out
mccortex/libs/samtools/test/mpileup/expected/70.out
mccortex/libs/samtools/test/mpileup/expected/71.out
mccortex/libs/samtools/test/mpileup/expected/72.out
mccortex/libs/samtools/test/mpileup/expected/73.out
mccortex/libs/samtools/test/mpileup/expected/74.out
mccortex/libs/samtools/test/mpileup/expected/75.out
mccortex/libs/samtools/test/mpileup/expected/76.out
mccortex/libs/samtools/test/mpileup/expected/77.out
mccortex/libs/samtools/test/mpileup/expected/8.out
mccortex/libs/samtools/test/mpileup/expected/9.out
mccortex/libs/samtools/test/mpileup/expected/d1_1.out
mccortex/libs/samtools/test/mpileup/expected/d1_12.out
mccortex/libs/samtools/test/mpileup/expected/d1_2.out
mccortex/libs/samtools/test/mpileup/expected/d2_12r.out
mccortex/libs/samtools/test/mpileup/expected/d3_12.out
mccortex/libs/samtools/test/mpileup/expected/d3_12r1a.out
mccortex/libs/samtools/test/mpileup/expected/d3_12r2a.out
mccortex/libs/samtools/test/mpileup/expected/d4_12.out
mccortex/libs/samtools/test/mpileup/expected/d4_12b.out
mccortex/libs/samtools/test/mpileup/expected/d4_12r.out
mccortex/libs/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
mccortex/libs/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
mccortex/libs/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
mccortex/libs/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
mccortex/libs/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
mccortex/libs/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
mccortex/libs/samtools/test/quickcheck/1.quickcheck.badeof.bam
mccortex/libs/samtools/test/quickcheck/2.quickcheck.badheader.bam
mccortex/libs/samtools/test/quickcheck/3.quickcheck.ok.bam
mccortex/libs/samtools/test/quickcheck/4.quickcheck.ok.bam
mccortex/libs/samtools/test/quickcheck/all.expected
mccortex/libs/samtools/test/reheader/1_view1.sam.expected
mccortex/libs/samtools/test/reheader/1_view1.sam.expected.err
mccortex/libs/samtools/test/reheader/2_view1.sam.expected
mccortex/libs/samtools/test/reheader/2_view1.sam.expected.err
mccortex/libs/samtools/test/reheader/3_view1.sam.expected
mccortex/libs/samtools/test/reheader/3_view1.sam.expected.err
mccortex/libs/samtools/test/reheader/hdr.sam
mccortex/libs/samtools/test/split/.gitignore
mccortex/libs/samtools/test/split/test_count_rg.c
mccortex/libs/samtools/test/split/test_expand_format_string.c
mccortex/libs/samtools/test/split/test_filter_header_rg.c
mccortex/libs/samtools/test/split/test_parse_args.c
mccortex/libs/samtools/test/stat/1.stats.expected
mccortex/libs/samtools/test/stat/10.stats.expected
mccortex/libs/samtools/test/stat/10_map_cigar.sam
mccortex/libs/samtools/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat
mccortex/libs/samtools/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat
mccortex/libs/samtools/test/stat/1_map_cigar.sam
mccortex/libs/samtools/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat
mccortex/libs/samtools/test/stat/2.stats.expected
mccortex/libs/samtools/test/stat/2_equal_cigar_full_seq.sam
mccortex/libs/samtools/test/stat/3.stats.expected
mccortex/libs/samtools/test/stat/3_map_cigar_equal_seq.sam
mccortex/libs/samtools/test/stat/4.stats.expected
mccortex/libs/samtools/test/stat/4_X_cigar_full_seq.sam
mccortex/libs/samtools/test/stat/5.stats.expected
mccortex/libs/samtools/test/stat/5_insert_cigar.sam
mccortex/libs/samtools/test/stat/6.stats.expected
mccortex/libs/samtools/test/stat/7.stats.expected
mccortex/libs/samtools/test/stat/7_supp.sam
mccortex/libs/samtools/test/stat/8.stats.expected
mccortex/libs/samtools/test/stat/8_secondary.sam
mccortex/libs/samtools/test/stat/9.stats.expected
mccortex/libs/samtools/test/stat/test.fa
mccortex/libs/samtools/test/stat/test.fa.fai
mccortex/libs/samtools/test/tview/test_get_rg_sample.c
mccortex/libs/samtools/win32/libcurses.a
mccortex/libs/samtools/win32/libz.a
mccortex/libs/samtools/win32/xcurses.h
mccortex/libs/samtools/win32/zconf.h
mccortex/libs/samtools/win32/zlib.h
mccortex/libs/seq-align/.gitignore
mccortex/libs/seq-align/.gitmodules
mccortex/libs/seq-align/.travis.yml
mccortex/libs/seq-align/Makefile
mccortex/libs/seq-align/README.md
mccortex/libs/seq-align/.git/FETCH_HEAD
mccortex/libs/seq-align/.git/HEAD
mccortex/libs/seq-align/.git/config
mccortex/libs/seq-align/.git/description
mccortex/libs/seq-align/.git/index
mccortex/libs/seq-align/.git/packed-refs
mccortex/libs/seq-align/.git/hooks/applypatch-msg.sample
mccortex/libs/seq-align/.git/hooks/commit-msg.sample
mccortex/libs/seq-align/.git/hooks/post-commit.sample
mccortex/libs/seq-align/.git/hooks/post-receive.sample
mccortex/libs/seq-align/.git/hooks/post-update.sample
mccortex/libs/seq-align/.git/hooks/pre-applypatch.sample
mccortex/libs/seq-align/.git/hooks/pre-commit.sample
mccortex/libs/seq-align/.git/hooks/pre-rebase.sample
mccortex/libs/seq-align/.git/hooks/prepare-commit-msg.sample
mccortex/libs/seq-align/.git/hooks/update.sample
mccortex/libs/seq-align/.git/info/exclude
mccortex/libs/seq-align/.git/logs/HEAD
mccortex/libs/seq-align/.git/logs/refs/heads/master
mccortex/libs/seq-align/.git/objects/pack/pack-9d7e22ca9d6d39ebf67e4f6e12fdae6193f16c3f.idx
mccortex/libs/seq-align/.git/objects/pack/pack-9d7e22ca9d6d39ebf67e4f6e12fdae6193f16c3f.pack
mccortex/libs/seq-align/.git/refs/heads/master
mccortex/libs/seq-align/.git/refs/remotes/origin/HEAD
mccortex/libs/seq-align/bin/lcs
mccortex/libs/seq-align/bin/needleman_wunsch
mccortex/libs/seq-align/bin/smith_waterman
mccortex/libs/seq-align/examples/Makefile
mccortex/libs/seq-align/examples/README.md
mccortex/libs/seq-align/examples/nw_cpp
mccortex/libs/seq-align/examples/nw_example
mccortex/libs/seq-align/examples/nw_example.c
mccortex/libs/seq-align/examples/nw_example.cpp
mccortex/libs/seq-align/examples/sw_cpp
mccortex/libs/seq-align/examples/sw_example
mccortex/libs/seq-align/examples/sw_example.c
mccortex/libs/seq-align/examples/sw_example.cpp
mccortex/libs/seq-align/libs/Makefile
mccortex/libs/seq-align/libs/bit_array/.gitignore
mccortex/libs/seq-align/libs/bit_array/.travis.yml
mccortex/libs/seq-align/libs/bit_array/AUTHORS
mccortex/libs/seq-align/libs/bit_array/LICENSE
mccortex/libs/seq-align/libs/bit_array/Makefile
mccortex/libs/seq-align/libs/bit_array/README.md
mccortex/libs/seq-align/libs/bit_array/bar.h
mccortex/libs/seq-align/libs/bit_array/bit_array.c
mccortex/libs/seq-align/libs/bit_array/bit_array.h
mccortex/libs/seq-align/libs/bit_array/bit_array.o
mccortex/libs/seq-align/libs/bit_array/bit_macros.h
mccortex/libs/seq-align/libs/bit_array/libbitarr.a
mccortex/libs/seq-align/libs/bit_array/.git/FETCH_HEAD
mccortex/libs/seq-align/libs/bit_array/.git/HEAD
mccortex/libs/seq-align/libs/bit_array/.git/config
mccortex/libs/seq-align/libs/bit_array/.git/description
mccortex/libs/seq-align/libs/bit_array/.git/index
mccortex/libs/seq-align/libs/bit_array/.git/packed-refs
mccortex/libs/seq-align/libs/bit_array/.git/hooks/applypatch-msg.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/commit-msg.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/post-commit.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/post-receive.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/post-update.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/pre-applypatch.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/pre-commit.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/pre-rebase.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/prepare-commit-msg.sample
mccortex/libs/seq-align/libs/bit_array/.git/hooks/update.sample
mccortex/libs/seq-align/libs/bit_array/.git/info/exclude
mccortex/libs/seq-align/libs/bit_array/.git/logs/HEAD
mccortex/libs/seq-align/libs/bit_array/.git/logs/refs/heads/master
mccortex/libs/seq-align/libs/bit_array/.git/objects/pack/pack-727b4cea6b299cc3473e2d2ae8fe0053af5b9e66.idx
mccortex/libs/seq-align/libs/bit_array/.git/objects/pack/pack-727b4cea6b299cc3473e2d2ae8fe0053af5b9e66.pack
mccortex/libs/seq-align/libs/bit_array/.git/refs/heads/master
mccortex/libs/seq-align/libs/bit_array/.git/refs/remotes/origin/HEAD
mccortex/libs/seq-align/libs/bit_array/dev/Makefile
mccortex/libs/seq-align/libs/bit_array/dev/bit_array_generate
mccortex/libs/seq-align/libs/bit_array/dev/bit_array_generate.c
mccortex/libs/seq-align/libs/bit_array/dev/bit_array_test
mccortex/libs/seq-align/libs/bit_array/dev/bit_array_test.c
mccortex/libs/seq-align/libs/bit_array/dev/bitlock_test
mccortex/libs/seq-align/libs/bit_array/dev/bitlock_test.c
mccortex/libs/seq-align/libs/bit_array/dev/bitlock_try_test
mccortex/libs/seq-align/libs/bit_array/dev/bitlock_try_test.c
mccortex/libs/seq-align/libs/bit_array/examples/Makefile
mccortex/libs/seq-align/libs/bit_array/examples/example.c
mccortex/libs/seq-align/libs/bit_array/examples/example.cpp
mccortex/libs/seq-align/libs/bit_array/examples/example_c
mccortex/libs/seq-align/libs/bit_array/examples/example_cpp
mccortex/libs/seq-align/libs/seq_file/.gitignore
mccortex/libs/seq-align/libs/seq_file/.travis.yml
mccortex/libs/seq-align/libs/seq_file/Makefile
mccortex/libs/seq-align/libs/seq_file/README.md
mccortex/libs/seq-align/libs/seq_file/seq_file.h
mccortex/libs/seq-align/libs/seq_file/stream_buffer.h
mccortex/libs/seq-align/libs/seq_file/.git/FETCH_HEAD
mccortex/libs/seq-align/libs/seq_file/.git/HEAD
mccortex/libs/seq-align/libs/seq_file/.git/config
mccortex/libs/seq-align/libs/seq_file/.git/description
mccortex/libs/seq-align/libs/seq_file/.git/index
mccortex/libs/seq-align/libs/seq_file/.git/packed-refs
mccortex/libs/seq-align/libs/seq_file/.git/hooks/applypatch-msg.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/commit-msg.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/post-commit.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/post-receive.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/post-update.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/pre-applypatch.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/pre-commit.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/pre-rebase.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/prepare-commit-msg.sample
mccortex/libs/seq-align/libs/seq_file/.git/hooks/update.sample
mccortex/libs/seq-align/libs/seq_file/.git/info/exclude
mccortex/libs/seq-align/libs/seq_file/.git/logs/HEAD
mccortex/libs/seq-align/libs/seq_file/.git/logs/refs/heads/master
mccortex/libs/seq-align/libs/seq_file/.git/objects/pack/pack-8a880262322a3e5ff26b4486a89464f1f87f6141.idx
mccortex/libs/seq-align/libs/seq_file/.git/objects/pack/pack-8a880262322a3e5ff26b4486a89464f1f87f6141.pack
mccortex/libs/seq-align/libs/seq_file/.git/refs/heads/master
mccortex/libs/seq-align/libs/seq_file/.git/refs/remotes/origin/HEAD
mccortex/libs/seq-align/libs/seq_file/benchmarks/Makefile
mccortex/libs/seq-align/libs/seq_file/benchmarks/kseq.h
mccortex/libs/seq-align/libs/seq_file/benchmarks/ktest
mccortex/libs/seq-align/libs/seq_file/benchmarks/ktest.c
mccortex/libs/seq-align/libs/seq_file/benchmarks/seq_test.c
mccortex/libs/seq-align/libs/seq_file/benchmarks/seqtest
mccortex/libs/seq-align/libs/seq_file/bin/dnacat
mccortex/libs/seq-align/libs/seq_file/dev/Makefile
mccortex/libs/seq-align/libs/seq_file/dev/seq_cmdline.c
mccortex/libs/seq-align/libs/seq_file/dev/seqcmdline
mccortex/libs/seq-align/libs/seq_file/scripts/perfect_covg.sh
mccortex/libs/seq-align/libs/seq_file/test/bad.fq
mccortex/libs/seq-align/libs/seq_file/test/mapped_fasta.bam
mccortex/libs/seq-align/libs/seq_file/test/mapped_fasta.sam
mccortex/libs/seq-align/libs/seq_file/test/mapped_fastq.bam
mccortex/libs/seq-align/libs/seq_file/test/mapped_fastq.sam
mccortex/libs/seq-align/libs/seq_file/test/multiline.fastq
mccortex/libs/seq-align/libs/seq_file/test/ncbi.fastq
mccortex/libs/seq-align/libs/seq_file/test/reads.fa
mccortex/libs/seq-align/libs/seq_file/test/reads.fq
mccortex/libs/seq-align/libs/seq_file/test/reads.txt
mccortex/libs/seq-align/libs/seq_file/test/single.txt
mccortex/libs/seq-align/libs/seq_file/test/small.fa
mccortex/libs/seq-align/libs/seq_file/test/small.fq
mccortex/libs/seq-align/libs/seq_file/test/small.txt
mccortex/libs/seq-align/libs/seq_file/tools/dna_cat.c
mccortex/libs/seq-align/libs/sort_r/.gitignore
mccortex/libs/seq-align/libs/sort_r/.travis.yml
mccortex/libs/seq-align/libs/sort_r/Makefile
mccortex/libs/seq-align/libs/sort_r/README.md
mccortex/libs/seq-align/libs/sort_r/example.c
mccortex/libs/seq-align/libs/sort_r/example_sort
mccortex/libs/seq-align/libs/sort_r/package.json
mccortex/libs/seq-align/libs/sort_r/sort_r.h
mccortex/libs/seq-align/libs/sort_r/travis.sh
mccortex/libs/seq-align/libs/sort_r/.git/FETCH_HEAD
mccortex/libs/seq-align/libs/sort_r/.git/HEAD
mccortex/libs/seq-align/libs/sort_r/.git/config
mccortex/libs/seq-align/libs/sort_r/.git/description
mccortex/libs/seq-align/libs/sort_r/.git/index
mccortex/libs/seq-align/libs/sort_r/.git/packed-refs
mccortex/libs/seq-align/libs/sort_r/.git/hooks/applypatch-msg.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/commit-msg.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/post-commit.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/post-receive.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/post-update.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/pre-applypatch.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/pre-commit.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/pre-rebase.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/prepare-commit-msg.sample
mccortex/libs/seq-align/libs/sort_r/.git/hooks/update.sample
mccortex/libs/seq-align/libs/sort_r/.git/info/exclude
mccortex/libs/seq-align/libs/sort_r/.git/logs/HEAD
mccortex/libs/seq-align/libs/sort_r/.git/logs/refs/heads/master
mccortex/libs/seq-align/libs/sort_r/.git/objects/pack/pack-47d61fc2ad05fa2995f1dc1e5ee63bf9f65a8352.idx
mccortex/libs/seq-align/libs/sort_r/.git/objects/pack/pack-47d61fc2ad05fa2995f1dc1e5ee63bf9f65a8352.pack
mccortex/libs/seq-align/libs/sort_r/.git/refs/heads/master
mccortex/libs/seq-align/libs/sort_r/.git/refs/remotes/origin/HEAD
mccortex/libs/seq-align/libs/string_buffer/.gitignore
mccortex/libs/seq-align/libs/string_buffer/.travis.yml
mccortex/libs/seq-align/libs/string_buffer/LICENSE
mccortex/libs/seq-align/libs/string_buffer/Makefile
mccortex/libs/seq-align/libs/string_buffer/README.md
mccortex/libs/seq-align/libs/string_buffer/libstrbuf.a
mccortex/libs/seq-align/libs/string_buffer/strbuf_test
mccortex/libs/seq-align/libs/string_buffer/strbuf_test.c
mccortex/libs/seq-align/libs/string_buffer/stream_buffer.h
mccortex/libs/seq-align/libs/string_buffer/string_buffer.c
mccortex/libs/seq-align/libs/string_buffer/string_buffer.h
mccortex/libs/seq-align/libs/string_buffer/string_buffer.o
mccortex/libs/seq-align/libs/string_buffer/.git/FETCH_HEAD
mccortex/libs/seq-align/libs/string_buffer/.git/HEAD
mccortex/libs/seq-align/libs/string_buffer/.git/config
mccortex/libs/seq-align/libs/string_buffer/.git/description
mccortex/libs/seq-align/libs/string_buffer/.git/index
mccortex/libs/seq-align/libs/string_buffer/.git/packed-refs
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/applypatch-msg.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/commit-msg.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/post-commit.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/post-receive.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/post-update.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/pre-applypatch.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/pre-commit.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/pre-rebase.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/prepare-commit-msg.sample
mccortex/libs/seq-align/libs/string_buffer/.git/hooks/update.sample
mccortex/libs/seq-align/libs/string_buffer/.git/info/exclude
mccortex/libs/seq-align/libs/string_buffer/.git/logs/HEAD
mccortex/libs/seq-align/libs/string_buffer/.git/logs/refs/heads/master
mccortex/libs/seq-align/libs/string_buffer/.git/objects/pack/pack-0bcb3969ce1d704ae752046ef96273bebf66533c.idx
mccortex/libs/seq-align/libs/string_buffer/.git/objects/pack/pack-0bcb3969ce1d704ae752046ef96273bebf66533c.pack
mccortex/libs/seq-align/libs/string_buffer/.git/refs/heads/master
mccortex/libs/seq-align/libs/string_buffer/.git/refs/remotes/origin/HEAD
mccortex/libs/seq-align/perl/NeedlemanWunsch.pm
mccortex/libs/seq-align/perl/SmithWaterman.pm
mccortex/libs/seq-align/perl/nw_example.pl
mccortex/libs/seq-align/perl/sw_example.pl
mccortex/libs/seq-align/scoring/BLOSUM100.txt
mccortex/libs/seq-align/scoring/BLOSUM30.txt
mccortex/libs/seq-align/scoring/BLOSUM35.txt
mccortex/libs/seq-align/scoring/BLOSUM40.txt
mccortex/libs/seq-align/scoring/BLOSUM45.txt
mccortex/libs/seq-align/scoring/BLOSUM50.txt
mccortex/libs/seq-align/scoring/BLOSUM55.txt
mccortex/libs/seq-align/scoring/BLOSUM60.txt
mccortex/libs/seq-align/scoring/BLOSUM62.txt
mccortex/libs/seq-align/scoring/BLOSUM65.txt
mccortex/libs/seq-align/scoring/BLOSUM70.txt
mccortex/libs/seq-align/scoring/BLOSUM75.txt
mccortex/libs/seq-align/scoring/BLOSUM80.txt
mccortex/libs/seq-align/scoring/BLOSUM85.txt
mccortex/libs/seq-align/scoring/BLOSUM90.txt
mccortex/libs/seq-align/scoring/BLOSUMN.txt
mccortex/libs/seq-align/scoring/DAYHOFF.txt
mccortex/libs/seq-align/scoring/GONNET.txt
mccortex/libs/seq-align/scoring/IDENTITY.txt
mccortex/libs/seq-align/scoring/MATCH.txt
mccortex/libs/seq-align/scoring/NUC.4.2.txt
mccortex/libs/seq-align/scoring/NUC.4.4.txt
mccortex/libs/seq-align/scoring/PAM10.txt
mccortex/libs/seq-align/scoring/PAM100.txt
mccortex/libs/seq-align/scoring/PAM110.txt
mccortex/libs/seq-align/scoring/PAM120.cdi.txt
mccortex/libs/seq-align/scoring/PAM120.txt
mccortex/libs/seq-align/scoring/PAM130.txt
mccortex/libs/seq-align/scoring/PAM140.txt
mccortex/libs/seq-align/scoring/PAM150.txt
mccortex/libs/seq-align/scoring/PAM160.cdi.txt
mccortex/libs/seq-align/scoring/PAM160.txt
mccortex/libs/seq-align/scoring/PAM170.txt
mccortex/libs/seq-align/scoring/PAM180.txt
mccortex/libs/seq-align/scoring/PAM190.txt
mccortex/libs/seq-align/scoring/PAM20.txt
mccortex/libs/seq-align/scoring/PAM200.cdi.txt
mccortex/libs/seq-align/scoring/PAM200.txt
mccortex/libs/seq-align/scoring/PAM210.txt
mccortex/libs/seq-align/scoring/PAM220.txt
mccortex/libs/seq-align/scoring/PAM230.txt
mccortex/libs/seq-align/scoring/PAM240.txt
mccortex/libs/seq-align/scoring/PAM250.cdi.txt
mccortex/libs/seq-align/scoring/PAM250.txt
mccortex/libs/seq-align/scoring/PAM260.txt
mccortex/libs/seq-align/scoring/PAM270.txt
mccortex/libs/seq-align/scoring/PAM280.txt
mccortex/libs/seq-align/scoring/PAM290.txt
mccortex/libs/seq-align/scoring/PAM30.txt
mccortex/libs/seq-align/scoring/PAM300.txt
mccortex/libs/seq-align/scoring/PAM310.txt
mccortex/libs/seq-align/scoring/PAM320.txt
mccortex/libs/seq-align/scoring/PAM330.txt
mccortex/libs/seq-align/scoring/PAM340.txt
mccortex/libs/seq-align/scoring/PAM350.txt
mccortex/libs/seq-align/scoring/PAM360.txt
mccortex/libs/seq-align/scoring/PAM370.txt
mccortex/libs/seq-align/scoring/PAM380.txt
mccortex/libs/seq-align/scoring/PAM390.txt
mccortex/libs/seq-align/scoring/PAM40.cdi.txt
mccortex/libs/seq-align/scoring/PAM40.txt
mccortex/libs/seq-align/scoring/PAM400.txt
mccortex/libs/seq-align/scoring/PAM410.txt
mccortex/libs/seq-align/scoring/PAM420.txt
mccortex/libs/seq-align/scoring/PAM430.txt
mccortex/libs/seq-align/scoring/PAM440.txt
mccortex/libs/seq-align/scoring/PAM450.txt
mccortex/libs/seq-align/scoring/PAM460.txt
mccortex/libs/seq-align/scoring/PAM470.txt
mccortex/libs/seq-align/scoring/PAM480.txt
mccortex/libs/seq-align/scoring/PAM490.txt
mccortex/libs/seq-align/scoring/PAM50.txt
mccortex/libs/seq-align/scoring/PAM500.txt
mccortex/libs/seq-align/scoring/PAM60.txt
mccortex/libs/seq-align/scoring/PAM70.txt
mccortex/libs/seq-align/scoring/PAM80.cdi.txt
mccortex/libs/seq-align/scoring/PAM80.txt
mccortex/libs/seq-align/scoring/PAM90.txt
mccortex/libs/seq-align/src/alignment.c
mccortex/libs/seq-align/src/alignment.h
mccortex/libs/seq-align/src/alignment.o
mccortex/libs/seq-align/src/alignment_cmdline.c
mccortex/libs/seq-align/src/alignment_cmdline.h
mccortex/libs/seq-align/src/alignment_cmdline.o
mccortex/libs/seq-align/src/alignment_macros.h
mccortex/libs/seq-align/src/alignment_scoring.c
mccortex/libs/seq-align/src/alignment_scoring.h
mccortex/libs/seq-align/src/alignment_scoring.o
mccortex/libs/seq-align/src/alignment_scoring_load.c
mccortex/libs/seq-align/src/alignment_scoring_load.h
mccortex/libs/seq-align/src/alignment_scoring_load.o
mccortex/libs/seq-align/src/libalign.a
mccortex/libs/seq-align/src/needleman_wunsch.c
mccortex/libs/seq-align/src/needleman_wunsch.h
mccortex/libs/seq-align/src/needleman_wunsch.o
mccortex/libs/seq-align/src/seq_align.h
mccortex/libs/seq-align/src/smith_waterman.c
mccortex/libs/seq-align/src/smith_waterman.h
mccortex/libs/seq-align/src/smith_waterman.o
mccortex/libs/seq-align/src/tools/lcs_cmdline.c
mccortex/libs/seq-align/src/tools/nw_cmdline.c
mccortex/libs/seq-align/src/tools/sw_cmdline.c
mccortex/libs/seq-align/src/tools/tests.c
mccortex/libs/seq_file/.gitignore
mccortex/libs/seq_file/.travis.yml
mccortex/libs/seq_file/Makefile
mccortex/libs/seq_file/README.md
mccortex/libs/seq_file/seq_file.h
mccortex/libs/seq_file/stream_buffer.h
mccortex/libs/seq_file/.git/FETCH_HEAD
mccortex/libs/seq_file/.git/HEAD
mccortex/libs/seq_file/.git/config
mccortex/libs/seq_file/.git/description
mccortex/libs/seq_file/.git/index
mccortex/libs/seq_file/.git/packed-refs
mccortex/libs/seq_file/.git/hooks/applypatch-msg.sample
mccortex/libs/seq_file/.git/hooks/commit-msg.sample
mccortex/libs/seq_file/.git/hooks/post-commit.sample
mccortex/libs/seq_file/.git/hooks/post-receive.sample
mccortex/libs/seq_file/.git/hooks/post-update.sample
mccortex/libs/seq_file/.git/hooks/pre-applypatch.sample
mccortex/libs/seq_file/.git/hooks/pre-commit.sample
mccortex/libs/seq_file/.git/hooks/pre-rebase.sample
mccortex/libs/seq_file/.git/hooks/prepare-commit-msg.sample
mccortex/libs/seq_file/.git/hooks/update.sample
mccortex/libs/seq_file/.git/info/exclude
mccortex/libs/seq_file/.git/logs/HEAD
mccortex/libs/seq_file/.git/logs/refs/heads/master
mccortex/libs/seq_file/.git/objects/pack/pack-8a880262322a3e5ff26b4486a89464f1f87f6141.idx
mccortex/libs/seq_file/.git/objects/pack/pack-8a880262322a3e5ff26b4486a89464f1f87f6141.pack
mccortex/libs/seq_file/.git/refs/heads/master
mccortex/libs/seq_file/.git/refs/remotes/origin/HEAD
mccortex/libs/seq_file/benchmarks/Makefile
mccortex/libs/seq_file/benchmarks/kseq.h
mccortex/libs/seq_file/benchmarks/ktest
mccortex/libs/seq_file/benchmarks/ktest.c
mccortex/libs/seq_file/benchmarks/seq_test.c
mccortex/libs/seq_file/benchmarks/seqtest
mccortex/libs/seq_file/bin/dnacat
mccortex/libs/seq_file/dev/Makefile
mccortex/libs/seq_file/dev/seq_cmdline.c
mccortex/libs/seq_file/dev/seqcmdline
mccortex/libs/seq_file/scripts/perfect_covg.sh
mccortex/libs/seq_file/test/bad.fq
mccortex/libs/seq_file/test/mapped_fasta.bam
mccortex/libs/seq_file/test/mapped_fasta.sam
mccortex/libs/seq_file/test/mapped_fastq.bam
mccortex/libs/seq_file/test/mapped_fastq.sam
mccortex/libs/seq_file/test/multiline.fastq
mccortex/libs/seq_file/test/ncbi.fastq
mccortex/libs/seq_file/test/reads.fa
mccortex/libs/seq_file/test/reads.fq
mccortex/libs/seq_file/test/reads.txt
mccortex/libs/seq_file/test/single.txt
mccortex/libs/seq_file/test/small.fa
mccortex/libs/seq_file/test/small.fq
mccortex/libs/seq_file/test/small.txt
mccortex/libs/seq_file/tools/dna_cat.c
mccortex/libs/sort_r/.gitignore
mccortex/libs/sort_r/.travis.yml
mccortex/libs/sort_r/Makefile
mccortex/libs/sort_r/README.md
mccortex/libs/sort_r/example.c
mccortex/libs/sort_r/example_sort
mccortex/libs/sort_r/package.json
mccortex/libs/sort_r/sort_r.h
mccortex/libs/sort_r/travis.sh
mccortex/libs/sort_r/.git/FETCH_HEAD
mccortex/libs/sort_r/.git/HEAD
mccortex/libs/sort_r/.git/config
mccortex/libs/sort_r/.git/description
mccortex/libs/sort_r/.git/index
mccortex/libs/sort_r/.git/packed-refs
mccortex/libs/sort_r/.git/hooks/applypatch-msg.sample
mccortex/libs/sort_r/.git/hooks/commit-msg.sample
mccortex/libs/sort_r/.git/hooks/post-commit.sample
mccortex/libs/sort_r/.git/hooks/post-receive.sample
mccortex/libs/sort_r/.git/hooks/post-update.sample
mccortex/libs/sort_r/.git/hooks/pre-applypatch.sample
mccortex/libs/sort_r/.git/hooks/pre-commit.sample
mccortex/libs/sort_r/.git/hooks/pre-rebase.sample
mccortex/libs/sort_r/.git/hooks/prepare-commit-msg.sample
mccortex/libs/sort_r/.git/hooks/update.sample
mccortex/libs/sort_r/.git/info/exclude
mccortex/libs/sort_r/.git/logs/HEAD
mccortex/libs/sort_r/.git/logs/refs/heads/master
mccortex/libs/sort_r/.git/objects/pack/pack-47d61fc2ad05fa2995f1dc1e5ee63bf9f65a8352.idx
mccortex/libs/sort_r/.git/objects/pack/pack-47d61fc2ad05fa2995f1dc1e5ee63bf9f65a8352.pack
mccortex/libs/sort_r/.git/refs/heads/master
mccortex/libs/sort_r/.git/refs/remotes/origin/HEAD
mccortex/libs/string_buffer/.gitignore
mccortex/libs/string_buffer/.travis.yml
mccortex/libs/string_buffer/LICENSE
mccortex/libs/string_buffer/Makefile
mccortex/libs/string_buffer/README.md
mccortex/libs/string_buffer/libstrbuf.a
mccortex/libs/string_buffer/strbuf_test
mccortex/libs/string_buffer/strbuf_test.c
mccortex/libs/string_buffer/stream_buffer.h
mccortex/libs/string_buffer/string_buffer.c
mccortex/libs/string_buffer/string_buffer.h
mccortex/libs/string_buffer/string_buffer.o
mccortex/libs/string_buffer/.git/FETCH_HEAD
mccortex/libs/string_buffer/.git/HEAD
mccortex/libs/string_buffer/.git/config
mccortex/libs/string_buffer/.git/description
mccortex/libs/string_buffer/.git/index
mccortex/libs/string_buffer/.git/packed-refs
mccortex/libs/string_buffer/.git/hooks/applypatch-msg.sample
mccortex/libs/string_buffer/.git/hooks/commit-msg.sample
mccortex/libs/string_buffer/.git/hooks/post-commit.sample
mccortex/libs/string_buffer/.git/hooks/post-receive.sample
mccortex/libs/string_buffer/.git/hooks/post-update.sample
mccortex/libs/string_buffer/.git/hooks/pre-applypatch.sample
mccortex/libs/string_buffer/.git/hooks/pre-commit.sample
mccortex/libs/string_buffer/.git/hooks/pre-rebase.sample
mccortex/libs/string_buffer/.git/hooks/prepare-commit-msg.sample
mccortex/libs/string_buffer/.git/hooks/update.sample
mccortex/libs/string_buffer/.git/info/exclude
mccortex/libs/string_buffer/.git/logs/HEAD
mccortex/libs/string_buffer/.git/logs/refs/heads/master
mccortex/libs/string_buffer/.git/objects/pack/pack-0bcb3969ce1d704ae752046ef96273bebf66533c.idx
mccortex/libs/string_buffer/.git/objects/pack/pack-0bcb3969ce1d704ae752046ef96273bebf66533c.pack
mccortex/libs/string_buffer/.git/refs/heads/master
mccortex/libs/string_buffer/.git/refs/remotes/origin/HEAD
mccortex/libs/vcf-slim/.gitignore
mccortex/libs/vcf-slim/Makefile
mccortex/libs/vcf-slim/README.md
mccortex/libs/vcf-slim/.git/FETCH_HEAD
mccortex/libs/vcf-slim/.git/HEAD
mccortex/libs/vcf-slim/.git/config
mccortex/libs/vcf-slim/.git/description
mccortex/libs/vcf-slim/.git/index
mccortex/libs/vcf-slim/.git/packed-refs
mccortex/libs/vcf-slim/.git/hooks/applypatch-msg.sample
mccortex/libs/vcf-slim/.git/hooks/commit-msg.sample
mccortex/libs/vcf-slim/.git/hooks/post-commit.sample
mccortex/libs/vcf-slim/.git/hooks/post-receive.sample
mccortex/libs/vcf-slim/.git/hooks/post-update.sample
mccortex/libs/vcf-slim/.git/hooks/pre-applypatch.sample
mccortex/libs/vcf-slim/.git/hooks/pre-commit.sample
mccortex/libs/vcf-slim/.git/hooks/pre-rebase.sample
mccortex/libs/vcf-slim/.git/hooks/prepare-commit-msg.sample
mccortex/libs/vcf-slim/.git/hooks/update.sample
mccortex/libs/vcf-slim/.git/info/exclude
mccortex/libs/vcf-slim/.git/logs/HEAD
mccortex/libs/vcf-slim/.git/logs/refs/heads/master
mccortex/libs/vcf-slim/.git/objects/04/5549df0a9fa01e8ca5f309a8c39b9e4868d66d
mccortex/libs/vcf-slim/.git/objects/05/6a5a197c5b033f04184377c59f17010fe13e7b
mccortex/libs/vcf-slim/.git/objects/07/33d7a9d65aa182d2b35d2d65f1788263e3bd61
mccortex/libs/vcf-slim/.git/objects/09/9efb1d6b7ce3a5892ebe1124ce1602ec22a462
mccortex/libs/vcf-slim/.git/objects/0d/1cc469fd4094dc4bb5a8829d8ba67f28f96773
mccortex/libs/vcf-slim/.git/objects/0f/9d20cd6d06cf50c9e5496cbc1efc7226668cbd
mccortex/libs/vcf-slim/.git/objects/19/1707d13ee812502af3f6662479b7221134f2cc
mccortex/libs/vcf-slim/.git/objects/1a/13ecb83a09e6fe673285f0374e29ea0324d59d
mccortex/libs/vcf-slim/.git/objects/1c/be3f0d483275cb2e5cd6901063f1effa186f24
mccortex/libs/vcf-slim/.git/objects/1d/58134171e87eafccd3e8bdb6d3536a151ecfe3
mccortex/libs/vcf-slim/.git/objects/1d/cfd70d778c42f24a99acd479cfca527aae8bb6
mccortex/libs/vcf-slim/.git/objects/23/8616adb0b745207d97d58d511f012459c007b9
mccortex/libs/vcf-slim/.git/objects/24/534edd4ab42f8c93d40a6ef0d45f1d67f9ca56
mccortex/libs/vcf-slim/.git/objects/29/de61daa471b0d36aaf50297def914ba6b0b9bc
mccortex/libs/vcf-slim/.git/objects/2b/c79e8970bc0e18799ec6d255c86cb7ce128065
mccortex/libs/vcf-slim/.git/objects/2e/b9d5dac8737973fc9b337487fe2d35bdf74ab1
mccortex/libs/vcf-slim/.git/objects/31/69bdc1dc50fc3e9bb55c39e691de88c90a8010
mccortex/libs/vcf-slim/.git/objects/31/76ebb84b298704b0f5631aaa0c2431d8898b16
mccortex/libs/vcf-slim/.git/objects/33/91dc8aa1f104c03711dc4b1f8afe2cf844bda7
mccortex/libs/vcf-slim/.git/objects/34/8d7d9c4b673cc1a9b35a7ac90074e9ee7746ed
mccortex/libs/vcf-slim/.git/objects/34/f61d62d0305f166ef7021a0d395379f00311e3
mccortex/libs/vcf-slim/.git/objects/35/1ba1a97315d0627475695cf135cf6f70c445dc
mccortex/libs/vcf-slim/.git/objects/36/852820c69c9eb5bb3bb96de7aeb15dda3f5578
mccortex/libs/vcf-slim/.git/objects/3d/074d9b4b943050c67eb91313d5bc9ecc43ec8c
mccortex/libs/vcf-slim/.git/objects/3e/72a716be79a5ada38ff427f9fac85ffab34ad3
mccortex/libs/vcf-slim/.git/objects/3f/9889fcdcd19a3a472c660cc6cc44a2fa6ac905
mccortex/libs/vcf-slim/.git/objects/40/85c086398971d38493230c6cdaf00f85c0e60d
mccortex/libs/vcf-slim/.git/objects/40/ee719398ef90a3564629dc8d8fea771ec41e2f
mccortex/libs/vcf-slim/.git/objects/42/f9632b9f67c82741a49c05f218f222b3a55021
mccortex/libs/vcf-slim/.git/objects/48/70a66768e62680b4b4f72406a4dcf3d66e5b30
mccortex/libs/vcf-slim/.git/objects/49/37b24ae0fbbae2d9957deeff35bf1396913fa0
mccortex/libs/vcf-slim/.git/objects/4a/9e704b71a4572706a77d3eccf477995fa82837
mccortex/libs/vcf-slim/.git/objects/4b/df50c3bf92b22d5d2385accab36d5e3441e315
mccortex/libs/vcf-slim/.git/objects/4c/215727313fc03b84d2df121a73f3b21a09074e
mccortex/libs/vcf-slim/.git/objects/50/bf5ed7bd5ac6dc8d82a3a8fad7f1c835506184
mccortex/libs/vcf-slim/.git/objects/54/d28e7a7b8e2b22ba3af5d07a11a22c476c8d76
mccortex/libs/vcf-slim/.git/objects/57/24668a6c5437d50c5a620c5cfc23682561fae5
mccortex/libs/vcf-slim/.git/objects/5c/bc8d5974659bd002d74730e3e0fa06b39b03bf
mccortex/libs/vcf-slim/.git/objects/60/da6930573a377861365fc534fcaf977f88069b
mccortex/libs/vcf-slim/.git/objects/61/8051d619dada6a817921f1808c83be46e9dae4
mccortex/libs/vcf-slim/.git/objects/64/f4aae6f0b6d7b8839522cfcbad87a9bbccc9ad
mccortex/libs/vcf-slim/.git/objects/65/9b76450869cb478538810f6caee6e2333a6a54
mccortex/libs/vcf-slim/.git/objects/69/536ec76af7866dde2449e9eb4ec5fe055d6738
mccortex/libs/vcf-slim/.git/objects/6d/cbab7546c3b6dbe9d6563d045b4f1f88e6fdfb
mccortex/libs/vcf-slim/.git/objects/72/68dab129e845c2a3eb9abeec880bef60b2ab56
mccortex/libs/vcf-slim/.git/objects/77/92cda45d07e6dd0d0da10f69d07fd782415cf0
mccortex/libs/vcf-slim/.git/objects/7c/0fea4d18bdb2e7e975de077b5ae324abf5d418
mccortex/libs/vcf-slim/.git/objects/7c/1b7cbdd3c54cdc7ca22c046a533849c1fef62d
mccortex/libs/vcf-slim/.git/objects/7c/fe1a2dbdd0503adb056726a0d71ac7aa7f6a89
mccortex/libs/vcf-slim/.git/objects/86/8791626dd004f82824504505d86f0f7b700a3c
mccortex/libs/vcf-slim/.git/objects/88/c2e3c5755a2b58c985962cc6685c8102640cbe
mccortex/libs/vcf-slim/.git/objects/8a/d8d9cd4c2a4c0a4aa6c101102b9b3aa3c4f949
mccortex/libs/vcf-slim/.git/objects/8d/991e55a2201b3ff6d918688c1f424e093d7373
mccortex/libs/vcf-slim/.git/objects/8f/328252d54871b3d0e3edf88c6ce18133a14d6d
mccortex/libs/vcf-slim/.git/objects/94/d8e42d87b9aa6837ecfcfa038db6708302fee5
mccortex/libs/vcf-slim/.git/objects/96/193b8a5b201a090961e52f3e4220ae11c71e28
mccortex/libs/vcf-slim/.git/objects/97/2759215d35c22e51b432e9ccf28cc084980bfd
mccortex/libs/vcf-slim/.git/objects/9a/1491b7a7e6c6cd18c3f6cf0fcd57eb1f0f1d34
mccortex/libs/vcf-slim/.git/objects/9a/8e75c03500dce53ae21c9d90139051e8c2958a
mccortex/libs/vcf-slim/.git/objects/9c/c9b1356ff20e2f2c86558b22f7b9413fd2bdc7
mccortex/libs/vcf-slim/.git/objects/9e/9937795eeeeb0fa5560564047badd9339587d7
mccortex/libs/vcf-slim/.git/objects/a0/b4ff2dfd69918cb1af2c6dedf1a9fc28d07d07
mccortex/libs/vcf-slim/.git/objects/a9/d3ecf563c1670368b997b1a2d4dae3546e87ec
mccortex/libs/vcf-slim/.git/objects/ac/522b9fe9728d0926bc4a711a3cef2570113ada
mccortex/libs/vcf-slim/.git/objects/ae/26c127040a4f5d15094c6965de1e8f754f2b78
mccortex/libs/vcf-slim/.git/objects/b9/96d136550673155fab80374702a4e91f5656cb
mccortex/libs/vcf-slim/.git/objects/bb/8c57d680f9b966b851ebd296a1936df8200a15
mccortex/libs/vcf-slim/.git/objects/bf/956ec219ec29ef6b6f8457139f67e6ef07ae48
mccortex/libs/vcf-slim/.git/objects/c1/c9256dd15aaf01a5a07603ac51017a660a27d0
mccortex/libs/vcf-slim/.git/objects/c3/d93269fe4200b884e253dde57bf274ac2e19c1
mccortex/libs/vcf-slim/.git/objects/c5/501a6adf5ada8aab5413cb873bed62c2334d18
mccortex/libs/vcf-slim/.git/objects/c5/676393b3bbafcc635329a7615a5e6e84ba9897
mccortex/libs/vcf-slim/.git/objects/c8/fddbc1e6414feeeeed643edbdc5f717a0ef0cf
mccortex/libs/vcf-slim/.git/objects/cb/8a96234a39e67774d27edde384ef8186f45fa9
mccortex/libs/vcf-slim/.git/objects/cc/bf79a6347b0409f18b6719cb3f6e8c62d6c3ab
mccortex/libs/vcf-slim/.git/objects/cd/3a9956302fe650730bbb7ac49789ba30b4905c
mccortex/libs/vcf-slim/.git/objects/ce/897d2d8f5ac01ebdddfdc21c2164f834518e6c
mccortex/libs/vcf-slim/.git/objects/d1/b1bbd91f9e899ffb31288f8d39e414fca3cf90
mccortex/libs/vcf-slim/.git/objects/d2/bc3bd163f8ce857fa70a0ecc567ddd7332cb93
mccortex/libs/vcf-slim/.git/objects/d3/9386d873032205a1dc807637501427e817ba0a
mccortex/libs/vcf-slim/.git/objects/dc/d497a7345d4ac0a0fb606db5bb2514d277dabd
mccortex/libs/vcf-slim/.git/objects/df/b573a8cef197d6cb89c1a5dd147730decfdcd4
mccortex/libs/vcf-slim/.git/objects/e0/ba799a791596281d18ab93277c4710f2e28f1e
mccortex/libs/vcf-slim/.git/objects/e1/0309bac7ad1c75ab06bc63fd7b90958c50df4d
mccortex/libs/vcf-slim/.git/objects/e1/d06aeb7974599e26d4c541127b97d91b385873
mccortex/libs/vcf-slim/.git/objects/e3/ebfdccedf88e19c7290838fcbef8d9a211659a
mccortex/libs/vcf-slim/.git/objects/e5/5bb1471fe6dcd92dfb266448e36e96fbae36e4
mccortex/libs/vcf-slim/.git/objects/f0/3b7cc1336d4dee41e2de8b36418cc57f317180
mccortex/libs/vcf-slim/.git/objects/f2/b62b638cf13471871dc24fbe41ebdf1b726f0d
mccortex/libs/vcf-slim/.git/objects/f5/d08dc3827b3c3f3e140de9581f22c9e98ecf48
mccortex/libs/vcf-slim/.git/objects/fc/b39dfe4e3e4893f8886ac54c706545a917f5b4
mccortex/libs/vcf-slim/.git/objects/fd/5871f427bb4bc0507a5684b1f182450f2e0f73
mccortex/libs/vcf-slim/.git/objects/fe/89e9ec54335363f3dad03fa9adcd918415a8ac
mccortex/libs/vcf-slim/.git/refs/heads/master
mccortex/libs/vcf-slim/.git/refs/remotes/origin/HEAD
mccortex/libs/vcf-slim/src/vcfcontigs.c
mccortex/libs/vcf-slim/src/vcfdist.c
mccortex/libs/vcf-slim/src/vcfhp.c
mccortex/libs/vcf-slim/tests/ans.vcf
mccortex/libs/vcf-slim/tests/in.vcf
mccortex/libs/vcf-slim/tests/ref.fa
mccortex/libs/vcf-slim/tests/sort.vcf
mccortex/libs/xxHash/.gitattributes
mccortex/libs/xxHash/.travis.yml
mccortex/libs/xxHash/LICENSE
mccortex/libs/xxHash/Makefile
mccortex/libs/xxHash/README.md
mccortex/libs/xxHash/xxh32sum
mccortex/libs/xxHash/xxh64sum
mccortex/libs/xxHash/xxhash.c
mccortex/libs/xxHash/xxhash.h
mccortex/libs/xxHash/xxhsum
mccortex/libs/xxHash/xxhsum.c
mccortex/libs/xxHash/.git/FETCH_HEAD
mccortex/libs/xxHash/.git/HEAD
mccortex/libs/xxHash/.git/config
mccortex/libs/xxHash/.git/description
mccortex/libs/xxHash/.git/index
mccortex/libs/xxHash/.git/packed-refs
mccortex/libs/xxHash/.git/hooks/applypatch-msg.sample
mccortex/libs/xxHash/.git/hooks/commit-msg.sample
mccortex/libs/xxHash/.git/hooks/post-commit.sample
mccortex/libs/xxHash/.git/hooks/post-receive.sample
mccortex/libs/xxHash/.git/hooks/post-update.sample
mccortex/libs/xxHash/.git/hooks/pre-applypatch.sample
mccortex/libs/xxHash/.git/hooks/pre-commit.sample
mccortex/libs/xxHash/.git/hooks/pre-rebase.sample
mccortex/libs/xxHash/.git/hooks/prepare-commit-msg.sample
mccortex/libs/xxHash/.git/hooks/update.sample
mccortex/libs/xxHash/.git/info/exclude
mccortex/libs/xxHash/.git/logs/HEAD
mccortex/libs/xxHash/.git/logs/refs/heads/dev
mccortex/libs/xxHash/.git/objects/pack/pack-5a8e3f244f3400da0a100fa73d2decebb0f3881e.idx
mccortex/libs/xxHash/.git/objects/pack/pack-5a8e3f244f3400da0a100fa73d2decebb0f3881e.pack
mccortex/libs/xxHash/.git/refs/heads/dev
mccortex/libs/xxHash/.git/refs/remotes/origin/HEAD
mccortex/libs/xxHash/cmake_unofficial/CMakeLists.txt
mccortex/results/README.txt
mccortex/results/NA12878/callcov/run.sh
mccortex/results/assembly/Makefile
mccortex/results/assembly/results/20150506.wed.txt
mccortex/results/assembly/results/20150511.mon.txt
mccortex/results/breakpoint_calling/Makefile
mccortex/results/breakpoint_calling/results/20150505.tues.txt
mccortex/results/breakpoint_calling/results/20150506.wed.txt
mccortex/results/breakpoint_calling/results/20150511.mon.hapdip.txt
mccortex/results/bubble_calling/Makefile
mccortex/results/bubble_calling/about.txt
mccortex/results/bubble_calling/cortex/Makefile
mccortex/results/bubble_calling/results/20150428.tues.k21.linux.txt
mccortex/results/bubble_calling/results/20150428.tues.k31.linux.txt
mccortex/results/bubble_calling/results/20150429.wed.k21.linux.txt
mccortex/results/bubble_calling/results/20150429.wed.k31.linux.txt
mccortex/results/bubble_calling/results/20150501.fri.run1.log
mccortex/results/bubble_calling/results/20150501.fri.run2.log
mccortex/results/bubble_calling/results/20150506.wed.txt
mccortex/results/bubble_calling/results/20150720/20150720_mon.log
mccortex/results/bubble_calling_10ecoli/Makefile
mccortex/results/bubble_calling_10ecoli/cortex/Makefile
mccortex/results/bubble_calling_10ecoli/results/20150510_sun_initrun/20150510.sun.txt
mccortex/results/bubble_calling_10ecoli/results/20150510_sun_initrun/20150510.sun.txt.2
mccortex/results/bubble_calling_10ecoli/results/20150510_sun_initrun/20150510.sun.txt.3
mccortex/results/bubble_calling_10ecoli/results/20150510_sun_initrun/20150510.sun.txt.4
mccortex/results/bubble_calling_10ecoli/results/20150615_joint_1by1_links_plain/20150617.wed.1by1.links.log
mccortex/results/bubble_calling_10ecoli/results/20150615_joint_1by1_links_plain/20150617.wed.1by1.plain.log
mccortex/results/bubble_calling_10ecoli/results/20150615_joint_1by1_links_plain/20150617.wed.joint.links.log
mccortex/results/bubble_calling_10ecoli/results/20150615_joint_1by1_links_plain/20150617.wed.joint.plain.log
mccortex/results/bubble_calling_10ecoli/results/20150615_joint_1by1_links_plain/20150617.wed.stats.txt
mccortex/results/bubble_calling_10ecoli/results/20150713_cortex/20150713_cortex.log
mccortex/results/bubble_calling_10ecoli/results/20150713_cortex/20150713_cortex.log.2
mccortex/results/bubble_calling_10ecoli/results/20150713_cortex/all.log
mccortex/results/contig_confidence/Makefile
mccortex/results/contig_confidence/confidence.tex
mccortex/results/contig_confidence/plot-confidence.R
mccortex/results/correct/ecoli/Makefile
mccortex/results/correct/hg_chr22/Makefile
mccortex/results/correct/hg_chr22/README.txt
mccortex/results/correct/hg_chr22/results/historic.results.txt
mccortex/results/correct/hg_chr22/results/results.20140926.txt
mccortex/results/data/download.sh
mccortex/results/data/PhiX/about.txt
mccortex/results/data/chr22/Makefile
mccortex/results/data/chr22/about.txt
mccortex/results/data/chr22/uniq_flanks/Makefile
mccortex/results/data/chr22/uniq_flanks/README.txt
mccortex/results/data/ecoli/Makefile
mccortex/results/data/ecoli/README.txt
mccortex/results/file_buffering/README.txt
mccortex/results/file_buffering/file-buffering.sh
mccortex/results/file_buffering/results20150413mon.mac.csv
mccortex/results/file_buffering/results20150413mon.mac.txt
mccortex/results/hash_table_benchmark/README.txt
mccortex/results/hash_table_benchmark/benchmark-tables.sh
mccortex/results/hash_table_benchmark/results20150409thurs.linux.log
mccortex/results/hash_table_benchmark/results20150409thurs.linux.txt
mccortex/results/hash_table_benchmark/results20150409thurs.mac.log
mccortex/results/hash_table_benchmark/results20150409thurs.mac.txt
mccortex/results/hash_table_benchmark/stats.R
mccortex/results/klebsiella/kleb_pneumoniae/assembly/get-max-covg.sh
mccortex/results/klebsiella/kleb_pneumoniae/assembly/make-dot-plots.sh
mccortex/results/klebsiella/kleb_pneumoniae/cortex/analysis.sh
mccortex/results/klebsiella/kleb_pneumoniae/cortex/call-cortex.sh
mccortex/results/klebsiella/kleb_pneumoniae/freebayes/analysis.sh
mccortex/results/klebsiella/kleb_pneumoniae/freebayes/freebayes.sh
mccortex/results/klebsiella/kleb_pneumoniae/indels/about.txt
mccortex/results/klebsiella/kleb_pneumoniae/indels/kleb-plot-hist.R
mccortex/results/klebsiella/kleb_pneumoniae/indels/run.sh
mccortex/results/klebsiella/kleb_pneumoniae/large_events/large-event-mappings.py
mccortex/results/klebsiella/kleb_pneumoniae/large_events/large-events-plot.R
mccortex/results/klebsiella/kleb_pneumoniae/mcrun/analysis.sh
mccortex/results/klebsiella/kleb_pneumoniae/platypus/analysis.sh
mccortex/results/klebsiella/kleb_pneumoniae/platypus/call-platypus.sh
mccortex/results/kmer_agnostic/Makefile
mccortex/results/kmer_agnostic/list-contig-lengths.sh
mccortex/results/kmer_agnostic/plot-kmer-err.R
mccortex/results/kmer_agnostic/plot-link-err.R
mccortex/results/kmer_agnostic/plot-results.R
mccortex/results/kmer_agnostic/run.sh
mccortex/results/kmer_agnostic/report/Makefile
mccortex/results/kmer_agnostic/report/kmer_agnostic.tex
mccortex/results/kmer_agnostic120/Makefile
mccortex/results/kmer_agnostic120/run.sh
mccortex/results/kmer_agnostic80/Makefile
mccortex/results/kmer_agnostic80/run.sh
mccortex/results/traversal_conjecture/Makefile
mccortex/results/traversal_conjecture/README.txt
mccortex/scripts/CortexBreakpoints.pm
mccortex/scripts/CortexBubbles.pm
mccortex/scripts/CortexGraph.pm
mccortex/scripts/CortexLinks.pm
mccortex/scripts/CortexScripts.pm
mccortex/scripts/LineReader.pm
mccortex/scripts/check-breakpoints.pl
mccortex/scripts/clean_bubbles.pl
mccortex/scripts/cortex_breakpoints.pl
mccortex/scripts/cortex_brkpnts_check_ref.pl
mccortex/scripts/cortex_bubbles.pl
mccortex/scripts/cortex_grab_links.pl
mccortex/scripts/cortex_links.pl
mccortex/scripts/cortex_mix_links.pl
mccortex/scripts/cortex_print_flanks.sh
mccortex/scripts/cortex_stats.pl
mccortex/scripts/cortex_to_graphviz.pl
mccortex/scripts/cortex_to_ray.sh
mccortex/scripts/ctx_contig_stats.pl
mccortex/scripts/ctx_kmer.pl
mccortex/scripts/find_maximal_substrings.pl
mccortex/scripts/links-bytes.sh
mccortex/scripts/links-count.sh
mccortex/scripts/longest-haplotype.sh
mccortex/scripts/make-circos.pl
mccortex/scripts/make-isec.sh
mccortex/scripts/make-pipeline.pl
mccortex/scripts/make-report.pl
mccortex/scripts/mccortex-bubbles-to-contigs.pl
mccortex/scripts/mccortex-header.pl
mccortex/scripts/mccortex-kcovg.pl
mccortex/scripts/mccortex-server.py
mccortex/scripts/median-link-threshold.sh
mccortex/scripts/multik-build.sh
mccortex/scripts/seq2pdf.sh
mccortex/scripts/thread_stats.pl
mccortex/scripts/update.sh
mccortex/scripts/R/get_auto_cleaning_cutoff.R
mccortex/scripts/R/gil_fit_cleaning_model.R
mccortex/scripts/R/install-deps.R
mccortex/scripts/R/link-cov-heatmap.R
mccortex/scripts/R/make_link_cutoffs.R
mccortex/scripts/R/plot-covg-hist.R
mccortex/scripts/R/plot-length-hist.R
mccortex/scripts/R/plot-link-counts.R
mccortex/scripts/R/plot-link-dist-cov.R
mccortex/scripts/analysis/calls-covg.pl
mccortex/scripts/analysis/gt-compare.pl
mccortex/scripts/analysis/haploid-sam-compare.py
mccortex/scripts/analysis/haploid-vcf-haplotypes.py
mccortex/scripts/analysis/mapping-vars-test.sh
mccortex/scripts/analysis/mummer-vcf-isec.sh
mccortex/scripts/analysis/mummer2vcf.sh
mccortex/scripts/analysis/sam-count-vars.pl
mccortex/scripts/calculations/bloom-filter-fpr.pl
mccortex/scripts/python/mccortex.py
mccortex/scripts/report/make-kmer-plot.sh
mccortex/scripts/report/make-link-plot.sh
mccortex/src/alignment/correct_alignment.c
mccortex/src/alignment/correct_alignment.h
mccortex/src/alignment/correct_aln_input.c
mccortex/src/alignment/correct_aln_input.h
mccortex/src/alignment/correct_aln_stats.c
mccortex/src/alignment/correct_aln_stats.h
mccortex/src/alignment/db_alignment.c
mccortex/src/alignment/db_alignment.h
mccortex/src/basic/aligned_call.c
mccortex/src/basic/aligned_call.h
mccortex/src/basic/async_read_io.c
mccortex/src/basic/async_read_io.h
mccortex/src/basic/binary_seq.c
mccortex/src/basic/binary_seq.h
mccortex/src/basic/call_file_reader.c
mccortex/src/basic/call_file_reader.h
mccortex/src/basic/chrom_pos_list.c
mccortex/src/basic/chrom_pos_list.h
mccortex/src/basic/cmd.c
mccortex/src/basic/cmd.h
mccortex/src/basic/common_buffers.h
mccortex/src/basic/decomp_breakpoint.c
mccortex/src/basic/decomp_breakpoint.h
mccortex/src/basic/decomp_bubble.c
mccortex/src/basic/decomp_bubble.h
mccortex/src/basic/dna.c
mccortex/src/basic/dna.h
mccortex/src/basic/file_filter.c
mccortex/src/basic/file_filter.h
mccortex/src/basic/file_util.c
mccortex/src/basic/file_util.h
mccortex/src/basic/graph_info.c
mccortex/src/basic/graph_info.h
mccortex/src/basic/hash.h
mccortex/src/basic/hash_mem.c
mccortex/src/basic/hash_mem.h
mccortex/src/basic/range.c
mccortex/src/basic/range.h
mccortex/src/basic/seq_loading_stats.c
mccortex/src/basic/seq_loading_stats.h
mccortex/src/basic/seq_reader.c
mccortex/src/basic/seq_reader.h
mccortex/src/basic/seqout.c
mccortex/src/basic/seqout.h
mccortex/src/basic/str_parsing.c
mccortex/src/basic/str_parsing.h
mccortex/src/commands/commands.h
mccortex/src/commands/ctx_breakpoints.c
mccortex/src/commands/ctx_bubbles.c
mccortex/src/commands/ctx_build.c
mccortex/src/commands/ctx_calls2vcf.c
mccortex/src/commands/ctx_clean.c
mccortex/src/commands/ctx_contigs.c
mccortex/src/commands/ctx_correct.c
mccortex/src/commands/ctx_coverage.c
mccortex/src/commands/ctx_dist_matrix.c
mccortex/src/commands/ctx_exp_abc.c
mccortex/src/commands/ctx_exp_hashtest.c
mccortex/src/commands/ctx_geno.c
mccortex/src/commands/ctx_health_check.c
mccortex/src/commands/ctx_index.c
mccortex/src/commands/ctx_infer_edges.c
mccortex/src/commands/ctx_join.c
mccortex/src/commands/ctx_links.c
mccortex/src/commands/ctx_pjoin.c
mccortex/src/commands/ctx_pop_bubbles.c
mccortex/src/commands/ctx_pview.c
mccortex/src/commands/ctx_reads.c
mccortex/src/commands/ctx_rmsubstr.c
mccortex/src/commands/ctx_server.c
mccortex/src/commands/ctx_sort.c
mccortex/src/commands/ctx_subgraph.c
mccortex/src/commands/ctx_thread.c
mccortex/src/commands/ctx_uniqkmers.c
mccortex/src/commands/ctx_unitigs.c
mccortex/src/commands/ctx_vcfcov.c
mccortex/src/commands/ctx_vcfgeno.c
mccortex/src/commands/ctx_view.c
mccortex/src/commands/read_thread_cmd.c
mccortex/src/commands/read_thread_cmd.h
mccortex/src/global/cortex_types.h
mccortex/src/global/ctx_alloc.c
mccortex/src/global/ctx_alloc.h
mccortex/src/global/ctx_assert.c
mccortex/src/global/ctx_assert.h
mccortex/src/global/ctx_output.c
mccortex/src/global/ctx_output.h
mccortex/src/global/global.c
mccortex/src/global/global.h
mccortex/src/global/util.c
mccortex/src/global/util.h
mccortex/src/global/version.h
mccortex/src/graph/binary_kmer.c
mccortex/src/graph/binary_kmer.h
mccortex/src/graph/cmd_mem.c
mccortex/src/graph/cmd_mem.h
mccortex/src/graph/contig_confidence.c
mccortex/src/graph/contig_confidence.h
mccortex/src/graph/db_graph.c
mccortex/src/graph/db_graph.h
mccortex/src/graph/db_node.c
mccortex/src/graph/db_node.h
mccortex/src/graph/graph_cache.c
mccortex/src/graph/graph_cache.h
mccortex/src/graph/graph_crawler.c
mccortex/src/graph/graph_crawler.h
mccortex/src/graph/graph_file_reader.c
mccortex/src/graph/graph_file_reader.h
mccortex/src/graph/graph_format.c
mccortex/src/graph/graph_format.h
mccortex/src/graph/graph_step.c
mccortex/src/graph/graph_step.h
mccortex/src/graph/graph_walker.c
mccortex/src/graph/graph_walker.h
mccortex/src/graph/graph_writer.c
mccortex/src/graph/graph_writer.h
mccortex/src/graph/graphs_load.c
mccortex/src/graph/graphs_load.h
mccortex/src/graph/hash_table.c
mccortex/src/graph/hash_table.h
mccortex/src/graph/json_hdr.c
mccortex/src/graph/json_hdr.h
mccortex/src/graph/kmer_occur.c
mccortex/src/graph/kmer_occur.h
mccortex/src/graph/prune_nodes.c
mccortex/src/graph/prune_nodes.h
mccortex/src/graph/repeat_walker.h
mccortex/src/graph/supernode.c
mccortex/src/graph/supernode.h
mccortex/src/graph/unitig_graph.c
mccortex/src/graph/unitig_graph.h
mccortex/src/graph/vcf_misc.c
mccortex/src/graph/vcf_misc.h
mccortex/src/graph_paths/gpath_checks.c
mccortex/src/graph_paths/gpath_checks.h
mccortex/src/graph_paths/gpath_reader.c
mccortex/src/graph_paths/gpath_reader.h
mccortex/src/graph_paths/gpath_save.c
mccortex/src/graph_paths/gpath_save.h
mccortex/src/kmer/kmer_hash.h
mccortex/src/kmer/kmer_size.c
mccortex/src/kmer/kmer_size.h
mccortex/src/main/debug.c
mccortex/src/main/mccortex.c
mccortex/src/main/tables.c
mccortex/src/main/tests.c
mccortex/src/paths/gpath.c
mccortex/src/paths/gpath.h
mccortex/src/paths/gpath_follow.c
mccortex/src/paths/gpath_follow.h
mccortex/src/paths/gpath_hash.c
mccortex/src/paths/gpath_hash.h
mccortex/src/paths/gpath_set.c
mccortex/src/paths/gpath_set.h
mccortex/src/paths/gpath_store.c
mccortex/src/paths/gpath_store.h
mccortex/src/paths/gpath_subset.c
mccortex/src/paths/gpath_subset.h
mccortex/src/paths/link_tree.c
mccortex/src/paths/link_tree.h
mccortex/src/tests/all_tests.c
mccortex/src/tests/all_tests.h
mccortex/src/tests/binary_seq_tests.c
mccortex/src/tests/bkmer_tests.c
mccortex/src/tests/bubble_caller_tests.c
mccortex/src/tests/build_graph_tests.c
mccortex/src/tests/cleaning_tests.c
mccortex/src/tests/corrected_aln_tests.c
mccortex/src/tests/dna_tests.c
mccortex/src/tests/graph_crawler_tests.c
mccortex/src/tests/graph_walker_tests.c
mccortex/src/tests/hash_table_tests.c
mccortex/src/tests/infer_edges_tests.c
mccortex/src/tests/kmer_occur_tests.c
mccortex/src/tests/node_tests.c
mccortex/src/tests/path_tests.c
mccortex/src/tests/repeat_walker_tests.c
mccortex/src/tests/subgraph_tests.c
mccortex/src/tests/supernode_tests.c
mccortex/src/tests/util_tests.c
mccortex/src/tools/assemble_contigs.c
mccortex/src/tools/assemble_contigs.h
mccortex/src/tools/assemble_stats.c
mccortex/src/tools/assemble_stats.h
mccortex/src/tools/breakpoint_caller.c
mccortex/src/tools/breakpoint_caller.h
mccortex/src/tools/bubble_caller.c
mccortex/src/tools/bubble_caller.h
mccortex/src/tools/build_graph.c
mccortex/src/tools/build_graph.h
mccortex/src/tools/clean_graph.c
mccortex/src/tools/clean_graph.h
mccortex/src/tools/correct_reads.c
mccortex/src/tools/correct_reads.h
mccortex/src/tools/generate_paths.c
mccortex/src/tools/generate_paths.h
mccortex/src/tools/genotyping.c
mccortex/src/tools/genotyping.h
mccortex/src/tools/infer_edges.c
mccortex/src/tools/infer_edges.h
mccortex/src/tools/pop_bubbles.c
mccortex/src/tools/pop_bubbles.h
mccortex/src/tools/subgraph.c
mccortex/src/tools/subgraph.h
mccortex/src/tools/vcf_coverage.c
mccortex/src/tools/vcf_coverage.h
mccortex/tests/run.sh
mccortex/tests/breakpoint/Makefile
mccortex/tests/breakpoint_empty/Makefile
mccortex/tests/bubble_one/Makefile
mccortex/tests/bubble_test/Makefile
mccortex/tests/bubble_test/truth.vcf
mccortex/tests/bubbles/Makefile
mccortex/tests/bubbles/bubbles1/Makefile
mccortex/tests/bubbles/bubbles2/Makefile
mccortex/tests/bubbles/bubbles2/itchy.fa
mccortex/tests/bubbles/bubbles2/make-exhaustive-alleles.py
mccortex/tests/bubbles/bubbles2/ref.fa
mccortex/tests/bubbles/bubbles2/scratchy.fa
mccortex/tests/bubbles/bubbles3/Makefile
mccortex/tests/build/Makefile
mccortex/tests/build/build0/Makefile
mccortex/tests/build/build1/Makefile
mccortex/tests/clean/Makefile
mccortex/tests/clean2/Makefile
mccortex/tests/clean3/Makefile
mccortex/tests/contigs/Makefile
mccortex/tests/correct/Makefile
mccortex/tests/coverage/Makefile
mccortex/tests/dist_matrix/Makefile
mccortex/tests/graphviz/Makefile
mccortex/tests/inferedges/Makefile
mccortex/tests/join/Makefile
mccortex/tests/largeK/Makefile
mccortex/tests/loop/Makefile
mccortex/tests/lossless/Makefile
mccortex/tests/lossless_reads/Makefile
mccortex/tests/old/calling_repeats/Makefile
mccortex/tests/path_check/Makefile
mccortex/tests/pipeline/Makefile
mccortex/tests/pjoin/Makefile
mccortex/tests/pop_bubbles1/Makefile
mccortex/tests/pop_bubbles2/Makefile
mccortex/tests/reads/Makefile
mccortex/tests/rmsubstr/Makefile
mccortex/tests/sort/Makefile
mccortex/tests/subgraph/Makefile
mccortex/tests/subgraph_supernodes/Makefile
mccortex/tests/supernodes/Makefile
mccortex/tests/thread2/Makefile
mccortex/tests/thread_pe/Makefile
mccortex/tests/thread_pe_short/Makefile
mccortex/tests/threading/Makefile
mccortex/tests/vcfcov/Makefile
mccortex/tests/vcfcov/calls0/Makefile
mccortex/tests/vcfcov/calls0/calls.vcf
mccortex/tests/vcfcov/calls0/truth.cov.vcf
mccortex/tests/vcfcov/calls1/Makefile
mccortex/tests/vcfcov/calls1/calls.vcf
mccortex/tests/vcfcov/calls1/jane.fa
mccortex/tests/vcfcov/calls1/john.fa
mccortex/tests/vcfcov/calls1/truth.cov.vcf
mccortex/tests/vcfcov/calls2/Makefile
mccortex/tests/vcfcov/calls2/calls.vcf
mccortex/tests/vcfcov/calls2/fake-vcf.py
mccortex/tests/vcfcov/calls2/sample.fa
mccortex/tests/vcfcov/calls2/truth.cov.vcf
mccortex/tests/vcfcov/calls3/Makefile
mccortex/tests/vcfcov/calls3/calls.vcf
mccortex/tests/vcfcov/calls3/hardy.fa
mccortex/tests/vcfcov/calls3/laurel.fa
mccortex/tests/vcfcov/calls3/truth.cov.vcf
mccortex/tests/vcfcov/calls4/Makefile
mccortex/tests/vcfcov/calls4/calls.vcf
mccortex/tests/vcfcov/calls4/fake-spaced-vcf.py
mccortex/tests/vcfcov/calls4/pluto.fa
mccortex/tests/vcfcov/calls4/truth.cov.vcf
mccortex/tests/vcfcov/calls5/Makefile
mccortex/tests/vcfcov/calls5/calls.vcf
mccortex/tests/vcfcov/calls5/truth.cov.vcf
mccortex/tests/vcfcov/ref/ref.fa
mccortex/travis/install.sh
mccortex/travis/script.sh
mykatlas/__init__.py
mykatlas/atlas_main.py
mykatlas/base.py
mykatlas/utils.py
mykatlas/version.py
mykatlas.egg-info/PKG-INFO
mykatlas.egg-info/SOURCES.txt
mykatlas.egg-info/dependency_links.txt
mykatlas.egg-info/entry_points.txt
mykatlas.egg-info/requires.txt
mykatlas.egg-info/top_level.txt
mykatlas/analysis/__init__.py
mykatlas/analysis/models.py
mykatlas/cmds/__init__.py
mykatlas/cmds/add-gt.py
mykatlas/cmds/add.py
mykatlas/cmds/atlasadd.py
mykatlas/cmds/diff.py
mykatlas/cmds/dump.py
mykatlas/cmds/genotype.py
mykatlas/cmds/makeprobes.py
mykatlas/cmds/place.py
mykatlas/cmds/walk.py
mykatlas/cortex/__init__.py
mykatlas/cortex/mccortex.py
mykatlas/cortex/server.py
mykatlas/stats/__init__.py
mykatlas/stats/stats.py
mykatlas/typing/__init__.py
mykatlas/typing/models/__init__.py
mykatlas/typing/models/base.py
mykatlas/typing/models/panel.py
mykatlas/typing/models/presence.py
mykatlas/typing/models/variant.py
mykatlas/typing/typer/__init__.py
mykatlas/typing/typer/base.py
mykatlas/typing/typer/genotyper.py
mykatlas/typing/typer/presence.py
mykatlas/typing/typer/variant.py