├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── README.md ├── annotations ├── ceph18.b37.exclude.2014-01-15.bed ├── ceph18.b37.include.2014-01-15.bed ├── ceph18.b37.lumpy.exclude.2014-01-15.bed ├── exclude.cnvnator_100bp.112015.bed └── exclude.cnvnator_100bp.GRCh38.20170403.bed ├── bin ├── annotate_rd.py ├── cnvnator_wrapper.py ├── speedseq └── speedseq.config ├── etc ├── add_storage-01.png ├── community_ami-01.png ├── instance_type-01.png ├── launch-01.png ├── speedseq-logo.png ├── speedseq-logo.svg └── speedseq_workflow.png ├── example ├── data │ ├── NA12878.20slice.30X.fastq.gz │ ├── human_g1k_v37_20_42220611-42542245.fasta │ ├── human_g1k_v37_20_42220611-42542245.fasta.amb │ ├── human_g1k_v37_20_42220611-42542245.fasta.ann │ ├── human_g1k_v37_20_42220611-42542245.fasta.bwt │ ├── human_g1k_v37_20_42220611-42542245.fasta.fai │ ├── human_g1k_v37_20_42220611-42542245.fasta.pac │ └── human_g1k_v37_20_42220611-42542245.fasta.sa ├── example_speedseq_install.sh └── run_speedseq.sh └── src ├── mbuffer ├── .hg_archival.txt ├── .hgtags ├── AUTHORS ├── ChangeLog ├── INSTALL ├── LICENSE ├── Makefile.in ├── NEWS ├── README ├── config.guess ├── config.h.in ├── config.sub ├── configure ├── configure.in ├── dest.h ├── install-sh ├── log.c ├── log.h ├── mbuffer.1.in ├── mbuffer.c ├── network.c └── network.h ├── sambamba └── samtools-1.3.1 ├── AUTHORS ├── ChangeLog.old ├── INSTALL ├── LICENSE ├── Makefile ├── Makefile.mingw ├── NEWS ├── README ├── aclocal.m4 ├── bam.c ├── bam.h ├── bam2bcf.c ├── bam2bcf.h ├── bam2bcf_indel.c ├── bam2depth.c ├── bam_addrprg.c ├── bam_aux.c ├── bam_cat.c ├── bam_color.c ├── bam_endian.h ├── bam_flags.c ├── bam_import.c ├── bam_index.c ├── bam_lpileup.c ├── bam_lpileup.h ├── bam_mate.c ├── bam_md.c ├── bam_plbuf.c ├── bam_plbuf.h ├── bam_plcmd.c ├── bam_quickcheck.c ├── bam_reheader.c ├── bam_rmdup.c ├── bam_rmdupse.c ├── bam_sort.c ├── bam_split.c ├── bam_stat.c ├── bam_tview.c ├── bam_tview.h ├── bam_tview_curses.c ├── bam_tview_html.c ├── bamshuf.c ├── bamtk.c ├── bedcov.c ├── bedidx.c ├── config.h.in ├── config.mk.in ├── configure ├── configure.ac ├── cut_target.c ├── dict.c ├── errmod.c ├── errmod.h ├── examples ├── 00README.txt ├── ex1.fa ├── toy.fa └── toy.sam ├── faidx.c ├── htslib-1.3.1 ├── INSTALL ├── LICENSE ├── Makefile ├── NEWS ├── README ├── bgzf.c ├── bgzip.c ├── config.h.in ├── config.mk.in ├── configure ├── configure.ac ├── cram │ ├── cram.h │ ├── cram_codecs.c │ ├── cram_codecs.h │ ├── cram_decode.c │ ├── cram_decode.h │ ├── cram_encode.c │ ├── cram_encode.h │ ├── cram_external.c │ ├── cram_index.c │ ├── cram_index.h │ ├── cram_io.c │ ├── cram_io.h │ ├── cram_samtools.c │ ├── cram_samtools.h │ ├── cram_stats.c │ ├── cram_stats.h │ ├── cram_structs.h │ ├── files.c │ ├── mFILE.c │ ├── mFILE.h │ ├── misc.h │ ├── open_trace_file.c │ ├── open_trace_file.h │ ├── os.h │ ├── pooled_alloc.c │ ├── pooled_alloc.h │ ├── rANS_byte.h │ ├── rANS_static.c │ ├── rANS_static.h │ ├── sam_header.c │ ├── sam_header.h │ ├── string_alloc.c │ ├── string_alloc.h │ ├── thread_pool.c │ ├── thread_pool.h │ ├── vlen.c │ ├── vlen.h │ ├── zfio.c │ └── zfio.h ├── faidx.5 ├── faidx.c ├── hfile.c ├── hfile_internal.h ├── hfile_irods.c ├── hfile_libcurl.c ├── hfile_net.c ├── hts.c ├── hts_internal.h ├── htsfile.1 ├── htsfile.c ├── htslib.mk ├── htslib.pc.in ├── htslib │ ├── bgzf.h │ ├── cram.h │ ├── faidx.h │ ├── hfile.h │ ├── hts.h │ ├── hts_defs.h │ ├── kbitset.h │ ├── kfunc.h │ ├── khash.h │ ├── khash_str2int.h │ ├── klist.h │ ├── knetfile.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.h │ ├── regidx.h │ ├── sam.h │ ├── synced_bcf_reader.h │ ├── tbx.h │ ├── vcf.h │ ├── vcf_sweep.h │ └── vcfutils.h ├── htslib_vars.mk ├── kfunc.c ├── knetfile.c ├── kstring.c ├── md5.c ├── plugin.c ├── regidx.c ├── sam.5 ├── sam.c ├── synced_bcf_reader.c ├── tabix.1 ├── tabix.c ├── tbx.c ├── test │ ├── aux#aux_java.cram │ ├── auxf#values.sam │ ├── auxf.fa │ ├── auxf.fa.fai │ ├── c1#bounds.sam │ ├── c1#clip.sam │ ├── c1#noseq.sam │ ├── c1#pad1.sam │ ├── c1#pad2.sam │ ├── c1#pad3.sam │ ├── c1#unknown.sam │ ├── c1.fa │ ├── c1.fa.fai │ ├── c2#pad.sam │ ├── c2.fa │ ├── c2.fa.fai │ ├── ce#1.sam │ ├── ce#2.sam │ ├── ce#5.sam │ ├── ce#5b.sam │ ├── ce#5b_java.cram │ ├── ce#large_seq.sam │ ├── ce#supp.sam │ ├── ce#tag_depadded.sam │ ├── ce#tag_padded.sam │ ├── ce#unmap.sam │ ├── ce#unmap1.sam │ ├── ce#unmap2.sam │ ├── ce.fa │ ├── ce.fa.fai │ ├── compare_sam.pl │ ├── cross_validate.sh │ ├── faidx.fa │ ├── fieldarith.c │ ├── fieldarith.sam │ ├── formatcols.vcf │ ├── hfile.c │ ├── noroundtrip-out.vcf │ ├── noroundtrip.vcf │ ├── sam.c │ ├── test-regidx.c │ ├── test-vcf-api.c │ ├── test-vcf-api.out │ ├── test-vcf-hdr-in.vcf │ ├── test-vcf-hdr.out │ ├── test-vcf-sweep.c │ ├── test-vcf-sweep.out │ ├── test.pl │ ├── test_view.c │ ├── xx#blank.sam │ ├── xx#large_aux.sam │ ├── xx#large_aux2.sam │ ├── xx#large_aux_java.cram │ ├── xx#minimal.sam │ ├── xx#pair.sam │ ├── xx#repeated.sam │ ├── xx#rg.sam │ ├── xx#tlen.sam │ ├── xx#tlen2.sam │ ├── xx#triplet.sam │ ├── xx#unsorted.sam │ ├── xx.fa │ └── xx.fa.fai ├── vcf.5 ├── vcf.c ├── vcf_sweep.c └── vcfutils.c ├── install-sh ├── kprobaln.c ├── kprobaln.h ├── misc ├── HmmGlocal.java ├── ace2sam.c ├── blast2sam.pl ├── bowtie2sam.pl ├── export2sam.pl ├── interpolate_sam.pl ├── maq2sam.c ├── md5fa.c ├── md5sum-lite.c ├── novo2sam.pl ├── plot-bamstats ├── psl2sam.pl ├── r2plot.lua ├── sam2vcf.pl ├── samtools.pl ├── seq_cache_populate.pl ├── soap2sam.pl ├── varfilter.py ├── vcfutils.lua ├── wgsim.1 ├── wgsim.c ├── wgsim_eval.pl └── zoom2sam.pl ├── padding.c ├── phase.c ├── sam.c ├── sam.h ├── sam_header.c ├── sam_header.h ├── sam_opts.c ├── sam_opts.h ├── sam_view.c ├── sample.c ├── sample.h ├── samtools.1 ├── samtools.h ├── stats.c ├── stats_isize.c ├── stats_isize.h ├── test ├── addrprg │ ├── 1_fixup.sam │ ├── 1_fixup.sam.expected │ ├── 1_fixup.sam.expected.err │ ├── 2_fixup_orphan.sam │ ├── 2_fixup_orphan.sam.expected │ ├── 2_fixup_orphan.sam.expected.err │ ├── 3_fixup.sam.expected │ ├── 3_fixup.sam.expected.err │ ├── 4_fixup_norg.sam │ ├── 4_fixup_norg.sam.expected │ └── 4_fixup_norg.sam.expected.err ├── bam2fq │ ├── 1.1.fq.expected │ ├── 1.2.fq.expected │ ├── 1.stdout.expected │ ├── 2.1.fq.expected │ ├── 2.2.fq.expected │ ├── 2.s.fq.expected │ ├── 2.stdout.expected │ ├── 3.1.fq.expected │ ├── 3.2.fq.expected │ ├── 3.s.fq.expected │ ├── 3.stdout.expected │ ├── 4.1.fq.expected │ ├── 4.2.fq.expected │ ├── 4.s.fq.expected │ └── 4.stdout.expected ├── dat │ ├── bam2fq.001.sam │ ├── bam2fq.002.sam │ ├── bam2fq.003.sam │ ├── cat.hdr │ ├── cram_md5 │ │ ├── 08c04d512d4797d9ba2a156c1daba468 │ │ ├── 7c35feac7036c1cdef3bee0cc4b21437 │ │ ├── 89b96de7acc5918c2858ef92710be7d4 │ │ └── 8a3d8deb9edd4ce3346b6061fcee6d0b │ ├── depad.001.fa │ ├── depad.001.fa.fai │ ├── depad.001p.sam │ ├── depad.001u.sam │ ├── dict.fa │ ├── dict.out │ ├── empty.expected │ ├── large_chrom.out │ ├── large_chrom.sam │ ├── large_chrom_bai_index.err │ ├── mpileup.1.sam │ ├── mpileup.2.sam │ ├── mpileup.3.sam │ ├── mpileup.err.1 │ ├── mpileup.out.1 │ ├── mpileup.out.2 │ ├── mpileup.out.3 │ ├── mpileup.out.4 │ ├── mpileup.ref.fa │ ├── mpileup.ref.fa.fai │ ├── test_input_1_a.bam │ ├── test_input_1_a.bam.bai.expected │ ├── test_input_1_a.sam │ ├── test_input_1_a_regex.sam │ ├── test_input_1_b.bam │ ├── test_input_1_b.sam │ ├── test_input_1_b_regex.sam │ ├── test_input_1_c.bam │ ├── test_input_1_c.sam │ ├── view.001.01.bed │ ├── view.001.02.bed │ ├── view.001.fa │ ├── view.001.fa.fai │ ├── view.001.sam │ ├── view.002.01.bed │ ├── view.002.02.bed │ ├── view.002.fa │ ├── view.002.fa.fai │ ├── view.002.sam │ ├── view.003.expected.sam │ └── view.003.sam ├── fixmate │ ├── 1_coord_sort.sam │ ├── 1_coord_sort.sam.expected │ ├── 1_coord_sort.sam.expected.err │ ├── 2_isize_overflow.sam │ ├── 2_isize_overflow.sam.expected │ ├── 3_reverse_read_pp_lt.sam │ ├── 3_reverse_read_pp_lt.sam.expected │ ├── 4_reverse_read_pp_equal.sam │ ├── 4_reverse_read_pp_equal.sam.expected │ ├── 5_ct.sam │ ├── 5_ct.sam.expected │ ├── 6_ct_replace.sam │ └── 6_ct_replace.sam.expected ├── idxstats │ ├── test_input_1_a.bam.expected │ └── test_input_1_a.bam.expected.err ├── merge │ ├── 2.merge.expected.bam │ ├── 3.merge.expected.bam │ ├── 3.merge.expected.err │ ├── 4.merge.expected.bam │ ├── 5.merge.expected.bam │ ├── 5.merge.expected.sam │ ├── 6.merge.expected.bam │ ├── 7.merge.expected.bam │ ├── test_3.fofn │ ├── test_bam_translate.c │ ├── test_header.sam │ ├── test_rtrans_build.c │ └── test_trans_tbl_init.c ├── mpileup │ ├── 1read.bam │ ├── 1read.sam │ ├── anomalous.sam │ ├── c1#ID.bam │ ├── c1#ID2.bam │ ├── c1#clip.bam │ ├── c1#pad1.bam │ ├── c1#pad2.bam │ ├── c1#pad3.bam │ ├── c1.fa │ ├── c1.fa.fai │ ├── ce#5b.bam │ ├── ce#5b.bam.bai │ ├── ce#5b.cram │ ├── ce#5b.cram.crai │ ├── ce#5b.sam │ ├── ce#large_seq.bam │ ├── ce#unmap.bam │ ├── ce#unmap1.bam │ ├── ce#unmap2.bam │ ├── ce.fa │ ├── ce.fa.fai │ ├── deep.sam │ ├── depth.reg │ ├── expected │ │ ├── 10.out │ │ ├── 11.out │ │ ├── 12.out │ │ ├── 13.out │ │ ├── 14.out │ │ ├── 15.out │ │ ├── 16.out │ │ ├── 17.out │ │ ├── 18.out │ │ ├── 19.out │ │ ├── 2.out │ │ ├── 20.out │ │ ├── 21.out │ │ ├── 22.out │ │ ├── 23.out │ │ ├── 24.out │ │ ├── 25.out │ │ ├── 26.out │ │ ├── 27.out │ │ ├── 28.out │ │ ├── 29.out │ │ ├── 3.out │ │ ├── 30.out │ │ ├── 31.out │ │ ├── 32.out │ │ ├── 33.out │ │ ├── 34.out │ │ ├── 35.out │ │ ├── 37.out │ │ ├── 38.out │ │ ├── 39.out │ │ ├── 4.out │ │ ├── 40.out │ │ ├── 41.out │ │ ├── 42.out │ │ ├── 43.out │ │ ├── 44.out │ │ ├── 45.out │ │ ├── 46.out │ │ ├── 47.out │ │ ├── 48.out │ │ ├── 49.out │ │ ├── 5.out │ │ ├── 50.out │ │ ├── 51.out │ │ ├── 52.out │ │ ├── 53.out │ │ ├── 54.out │ │ ├── 55.out │ │ ├── 56.out │ │ ├── 57.out │ │ ├── 58.out │ │ ├── 59.out │ │ ├── 6.out │ │ ├── 60.out │ │ ├── 61.out │ │ ├── 62.out │ │ ├── 63.out │ │ ├── 64.out │ │ ├── 65.out │ │ ├── 66.out │ │ ├── 67.out │ │ ├── 68.out │ │ ├── 69.out │ │ ├── 7.out │ │ ├── 70.out │ │ ├── 71.out │ │ ├── 72.out │ │ ├── 73.out │ │ ├── 74.out │ │ ├── 75.out │ │ ├── 76.out │ │ ├── 77.out │ │ ├── 8.out │ │ ├── 9.out │ │ ├── d1_1.out │ │ ├── d1_12.out │ │ ├── d1_2.out │ │ ├── d2_12r.out │ │ ├── d3_12.out │ │ ├── d3_12r1a.out │ │ ├── d3_12r2a.out │ │ ├── d4_12.out │ │ ├── d4_12b.out │ │ └── d4_12r.out │ ├── indels.sam │ ├── md5 │ │ ├── 02099b2aad2cfe707759353724fb40ae │ │ ├── 0d4dfc45807d6a11439e858605cb364d │ │ ├── 351f64d4f4f9ddd45b35336ad97aa6de │ │ ├── 6ec590eb82c361a61e6baabce20109bc │ │ ├── 6f60cdf4c739651ae72d53e2e94825c1 │ │ └── 73d180d5cb3860a2713927b6812eab0e │ ├── mpileup-E.bam │ ├── mpileup.1.bam │ ├── mpileup.1.bam.bai │ ├── mpileup.2.bam │ ├── mpileup.3.bam │ ├── mpileup.ref.fa │ ├── mpileup.ref.fa.fai │ ├── mpileup.reg │ ├── overlap50.sam │ ├── overlapIllumina.bam │ ├── regions │ ├── regression.sh │ ├── xx#depth1.sam │ ├── xx#depth2.sam │ ├── xx#minimal.bam │ ├── xx#triplet.bam │ ├── xx.bed │ ├── xx.bed2 │ ├── xx.fa │ └── xx.fa.fai ├── quickcheck │ ├── 1.quickcheck.badeof.bam │ ├── 2.quickcheck.badheader.bam │ ├── 3.quickcheck.ok.bam │ ├── 4.quickcheck.ok.bam │ ├── 5.quickcheck.truncated.cram │ └── all.expected ├── reheader │ ├── 1_view1.sam.expected │ ├── 1_view1.sam.expected.err │ ├── 2_view1.sam.expected │ ├── 2_view1.sam.expected.err │ ├── 3_view1.sam.expected │ ├── 3_view1.sam.expected.err │ └── hdr.sam ├── split │ ├── test_count_rg.c │ ├── test_expand_format_string.c │ ├── test_filter_header_rg.c │ └── test_parse_args.c ├── stat │ ├── 1.stats.expected │ ├── 10.stats.expected │ ├── 10_map_cigar.sam │ ├── 10_map_cigar.sam_s1_a_1.expected.bamstat │ ├── 10_map_cigar.sam_s1_b_1.expected.bamstat │ ├── 1_map_cigar.sam │ ├── 1_map_cigar.sam_s1_a_1.expected.bamstat │ ├── 2.stats.expected │ ├── 2_equal_cigar_full_seq.sam │ ├── 3.stats.expected │ ├── 3_map_cigar_equal_seq.sam │ ├── 4.stats.expected │ ├── 4_X_cigar_full_seq.sam │ ├── 5.stats.expected │ ├── 5_insert_cigar.sam │ ├── 6.stats.expected │ ├── 7.stats.expected │ ├── 7_supp.sam │ ├── 8.stats.expected │ ├── 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