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requirements.txt
setup.py
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mccortex/.travis.yml
mccortex/AUTHORS
mccortex/LICENSE
mccortex/Makefile
mccortex/README.md
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/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
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mccortex/libs/bcftools/HMM.h
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mccortex/libs/bcftools/ccall.c
mccortex/libs/bcftools/consensus.c
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mccortex/libs/bcftools/khash_str2str.h
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mccortex/libs/bcftools/mcall.c
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mccortex/libs/bioinf-perl/.git
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mccortex/libs/bioinf-perl/cortex_scripts/cortex_aligned_reads.pl
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mccortex/libs/htslib/test/test-regidx
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mccortex/libs/htslib/test/test-regidx.o
mccortex/libs/htslib/test/test-vcf-api
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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
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mccortex/libs/htslib/test/test-vcf-sweep.o
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mccortex/libs/htslib/test/xx#blank.sam
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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/.git
mccortex/libs/madcrowlib/.gitignore
mccortex/libs/madcrowlib/.travis.yml
mccortex/libs/madcrowlib/LICENSE
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mccortex/libs/madcrowlib/madcrow_linkedlist.h
mccortex/libs/madcrowlib/madcrow_list.h
mccortex/libs/madcrowlib/madcrowlib.h
mccortex/libs/madcrowlib/run_tests
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mccortex/libs/maximal_substrs/Makefile
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mccortex/libs/misc/Makefile
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mccortex/libs/msg-pool/.git
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mccortex/libs/readsim/.git
mccortex/libs/readsim/.gitignore
mccortex/libs/readsim/Makefile
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mccortex/libs/readsim/seq_file.h
mccortex/libs/readsim/stream_buffer.h
mccortex/libs/samtools/.git
mccortex/libs/samtools/.gitattributes
mccortex/libs/samtools/.gitignore
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mccortex/libs/samtools/AUTHORS
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mccortex/libs/samtools/Makefile.mingw
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mccortex/libs/samtools/bam.c
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mccortex/libs/samtools/bam2bcf.c
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mccortex/libs/samtools/bam2bcf_indel.c
mccortex/libs/samtools/bam2depth.c
mccortex/libs/samtools/bam_addrprg.c
mccortex/libs/samtools/bam_aux.c
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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
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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
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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
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mccortex/libs/samtools/stats.c
mccortex/libs/samtools/stats_isize.c
mccortex/libs/samtools/stats_isize.h
mccortex/libs/samtools/.travis/clone
mccortex/libs/samtools/examples/.gitignore
mccortex/libs/samtools/examples/00README.txt
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mccortex/libs/samtools/examples/toy.fa
mccortex/libs/samtools/examples/toy.sam
mccortex/libs/samtools/misc/HmmGlocal.java
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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
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mccortex/libs/samtools/test/dat/depad.001u.sam
mccortex/libs/samtools/test/dat/dict.fa
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mccortex/libs/samtools/test/dat/empty.expected
mccortex/libs/samtools/test/dat/large_chrom.out
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mccortex/libs/samtools/test/dat/large_chrom_bai_index.err
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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
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mccortex/libs/samtools/test/dat/mpileup.out.3
mccortex/libs/samtools/test/dat/mpileup.out.4
mccortex/libs/samtools/test/dat/mpileup.ref.fa
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mccortex/libs/samtools/test/dat/test_input_1_a.bam
mccortex/libs/samtools/test/dat/test_input_1_a.bam.bai.expected
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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
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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
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mccortex/libs/samtools/test/mpileup/.gitignore
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