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MANIFEST.in
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MANIFEST.in
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include bsbolt/External/WGSIM/src/kseq.h
include bsbolt/External/WGSIM/src/wgsim.cpp
include bsbolt/External/WGSIM/Makefile
include bsbolt/External/BWA/bntseq.c
include bsbolt/External/BWA/bntseq.h
include bsbolt/External/BWA/bs_helpers.cpp
include bsbolt/External/BWA/bs_helpers.h
include bsbolt/External/BWA/bs_sorter.cpp
include bsbolt/External/BWA/bs_sorter.h
include bsbolt/External/BWA/bs_sorter_wrapper.cpp
include bsbolt/External/BWA/bs_sorter_wrapper.h
include bsbolt/External/BWA/bwa.c
include bsbolt/External/BWA/bwa.h
include bsbolt/External/BWA/bwamem.c
include bsbolt/External/BWA/bwamem.h
include bsbolt/External/BWA/bwamem_extra.c
include bsbolt/External/BWA/bwamem_pair.c
include bsbolt/External/BWA/bwashm.c
include bsbolt/External/BWA/bwt.c
include bsbolt/External/BWA/bwt.h
include bsbolt/External/BWA/bwt_gen.c
include bsbolt/External/BWA/bwtindex.c
include bsbolt/External/BWA/COPYING
include bsbolt/External/BWA/fastmap.c
include bsbolt/External/BWA/fastmap.h
include bsbolt/External/BWA/is.c
include bsbolt/External/BWA/kbtree.h
include bsbolt/External/BWA/khash.h
include bsbolt/External/BWA/kopen.c
include bsbolt/External/BWA/kseq.h
include bsbolt/External/BWA/ksort.h
include bsbolt/External/BWA/kstring.c
include bsbolt/External/BWA/kstring.h
include bsbolt/External/BWA/ksw.c
include bsbolt/External/BWA/ksw.h
include bsbolt/External/BWA/kthread.c
include bsbolt/External/BWA/kvec.h
include bsbolt/External/BWA/main.c
include bsbolt/External/BWA/Makefile
include bsbolt/External/BWA/malloc_wrap.c
include bsbolt/External/BWA/malloc_wrap.h
include bsbolt/External/BWA/QSufSort.c
include bsbolt/External/BWA/QSufSort.h
include bsbolt/External/BWA/rle.c
include bsbolt/External/BWA/rle.h
include bsbolt/External/BWA/rope.c
include bsbolt/External/BWA/rope.h
include bsbolt/External/BWA/utils.c
include bsbolt/External/BWA/utils.h
include bsbolt/External/HTSLIB/kfunc.c
include bsbolt/External/HTSLIB/bcf_sr_sort.h
include bsbolt/External/HTSLIB/regidx.c
include bsbolt/External/HTSLIB/tabix.c
include bsbolt/External/HTSLIB/INSTALL
include bsbolt/External/HTSLIB/errmod.c
include bsbolt/External/HTSLIB/hts.c
include bsbolt/External/HTSLIB/stream_bam.c
include bsbolt/External/HTSLIB/Makefile
include bsbolt/External/HTSLIB/sam.c
include bsbolt/External/HTSLIB/md5.c
include bsbolt/External/HTSLIB/header.c
include bsbolt/External/HTSLIB/vcf_sweep.c
include bsbolt/External/HTSLIB/thread_pool.c
include bsbolt/External/HTSLIB/sam_internal.h
include bsbolt/External/HTSLIB/textutils.c
include bsbolt/External/HTSLIB/synced_bcf_reader.c
include bsbolt/External/HTSLIB/LICENSE
include bsbolt/External/HTSLIB/hfile_internal.h
include bsbolt/External/HTSLIB/htslib_vars.mk
include bsbolt/External/HTSLIB/vcf.c
include bsbolt/External/HTSLIB/htslib.mk
include bsbolt/External/HTSLIB/bcf_sr_sort.c
include bsbolt/External/HTSLIB/probaln.c
include bsbolt/External/HTSLIB/config.mk.in
include bsbolt/External/HTSLIB/header.h
include bsbolt/External/HTSLIB/vcfutils.c
include bsbolt/External/HTSLIB/kstring.c
include bsbolt/External/HTSLIB/tabix.1
include bsbolt/External/HTSLIB/bgzf.c
include bsbolt/External/HTSLIB/hts_os.c
include bsbolt/External/HTSLIB/region.c
include bsbolt/External/HTSLIB/hts_internal.h
include bsbolt/External/HTSLIB/htslib.pc.in
include bsbolt/External/HTSLIB/hfile_net.c
include bsbolt/External/HTSLIB/knetfile.c
include bsbolt/External/HTSLIB/realn.c
include bsbolt/External/HTSLIB/htslib-s3-plugin.7
include bsbolt/External/HTSLIB/faidx.c
include bsbolt/External/HTSLIB/hfile.c
include bsbolt/External/HTSLIB/multipart.c
include bsbolt/External/HTSLIB/sam.5
include bsbolt/External/HTSLIB/configure.ac
include bsbolt/External/HTSLIB/vcf.5
include bsbolt/External/HTSLIB/hfile_s3_write.c
include bsbolt/External/HTSLIB/version.sh
include bsbolt/External/HTSLIB/textutils_internal.h
include bsbolt/External/HTSLIB/tbx.c
include bsbolt/External/HTSLIB/htsfile.1
include bsbolt/External/HTSLIB/thread_pool_internal.h
include bsbolt/External/HTSLIB/plugin.c
include bsbolt/External/HTSLIB/hfile_s3.c
include bsbolt/External/HTSLIB/bgzip.1
include bsbolt/External/HTSLIB/hfile_libcurl.c
include bsbolt/External/HTSLIB/hfile_gcs.c
include bsbolt/External/HTSLIB/faidx.5
include bsbolt/External/HTSLIB/htsfile.c
include bsbolt/External/HTSLIB/bgzip.c
include bsbolt/External/HTSLIB/os/lzma_stub.h
include bsbolt/External/HTSLIB/os/rand.c
include bsbolt/External/HTSLIB/htslib/khash.h
include bsbolt/External/HTSLIB/htslib/kseq.h
include bsbolt/External/HTSLIB/htslib/sam.h
include bsbolt/External/HTSLIB/htslib/khash_str2int.h
include bsbolt/External/HTSLIB/htslib/hts_endian.h
include bsbolt/External/HTSLIB/htslib/cram.h
include bsbolt/External/HTSLIB/htslib/tbx.h
include bsbolt/External/HTSLIB/htslib/kbitset.h
include bsbolt/External/HTSLIB/htslib/synced_bcf_reader.h
include bsbolt/External/HTSLIB/htslib/vcf.h
include bsbolt/External/HTSLIB/htslib/kroundup.h
include bsbolt/External/HTSLIB/htslib/vcf_sweep.h
include bsbolt/External/HTSLIB/htslib/kstring.h
include bsbolt/External/HTSLIB/htslib/bgzf.h
include bsbolt/External/HTSLIB/htslib/hts_defs.h
include bsbolt/External/HTSLIB/htslib/hts_log.h
include bsbolt/External/HTSLIB/htslib/vcfutils.h
include bsbolt/External/HTSLIB/htslib/thread_pool.h
include bsbolt/External/HTSLIB/htslib/hts.h
include bsbolt/External/HTSLIB/htslib/kfunc.h
include bsbolt/External/HTSLIB/htslib/hts_os.h
include bsbolt/External/HTSLIB/htslib/faidx.h
include bsbolt/External/HTSLIB/htslib/knetfile.h
include bsbolt/External/HTSLIB/htslib/ksort.h
include bsbolt/External/HTSLIB/htslib/hfile.h
include bsbolt/External/HTSLIB/htslib/klist.h
include bsbolt/External/HTSLIB/htslib/regidx.h
include bsbolt/External/HTSLIB/m4/hts_prog_cc_warnings.m4
include bsbolt/External/HTSLIB/m4/hts_hide_dynamic_syms.m4
include bsbolt/External/HTSLIB/m4/pkg.m4
include bsbolt/External/HTSLIB/cram/cram_encode.h
include bsbolt/External/HTSLIB/cram/mFILE.c
include bsbolt/External/HTSLIB/cram/cram_io.c
include bsbolt/External/HTSLIB/cram/cram_decode.h
include bsbolt/External/HTSLIB/cram/cram.h
include bsbolt/External/HTSLIB/cram/mFILE.h
include bsbolt/External/HTSLIB/cram/cram_io.h
include bsbolt/External/HTSLIB/cram/string_alloc.h
include bsbolt/External/HTSLIB/cram/cram_index.c
include bsbolt/External/HTSLIB/cram/cram_samtools.c
include bsbolt/External/HTSLIB/cram/misc.h
include bsbolt/External/HTSLIB/cram/open_trace_file.h
include bsbolt/External/HTSLIB/cram/cram_external.c
include bsbolt/External/HTSLIB/cram/cram_decode.c
include bsbolt/External/HTSLIB/cram/cram_samtools.h
include bsbolt/External/HTSLIB/cram/open_trace_file.c
include bsbolt/External/HTSLIB/cram/pooled_alloc.h
include bsbolt/External/HTSLIB/cram/cram_encode.c
include bsbolt/External/HTSLIB/cram/rANS_static.c
include bsbolt/External/HTSLIB/cram/rANS_byte.h
include bsbolt/External/HTSLIB/cram/string_alloc.c
include bsbolt/External/HTSLIB/cram/pooled_alloc.c
include bsbolt/External/HTSLIB/cram/cram_stats.h
include bsbolt/External/HTSLIB/cram/cram_structs.h
include bsbolt/External/HTSLIB/cram/cram_index.h
include bsbolt/External/HTSLIB/cram/cram_codecs.c
include bsbolt/External/HTSLIB/cram/cram_stats.c
include bsbolt/External/HTSLIB/cram/os.h
include bsbolt/External/HTSLIB/cram/cram_codecs.h
include bsbolt/External/HTSLIB/cram/rANS_static.h
include bsbolt/External/HTSLIB/test/thrash_threads6.c
include bsbolt/External/HTSLIB/test/xx#tlen.sam
include bsbolt/External/HTSLIB/test/index.bam.bai
include bsbolt/External/HTSLIB/test/xx#rg.sam
include bsbolt/External/HTSLIB/test/xx#pair.sam
include bsbolt/External/HTSLIB/test/fieldarith.c
include bsbolt/External/HTSLIB/test/test-bcf-translate.c
include bsbolt/External/HTSLIB/test/ce#1.sam
include bsbolt/External/HTSLIB/test/test-bcf-sr.pl
include bsbolt/External/HTSLIB/test/realn02_exp.sam
include bsbolt/External/HTSLIB/test/md.fa
include bsbolt/External/HTSLIB/test/test-logging.pl
include bsbolt/External/HTSLIB/test/realn02.fa.fai
include bsbolt/External/HTSLIB/test/xx#blank.sam
include bsbolt/External/HTSLIB/test/no_hdr_sq_1.expected.sam
include bsbolt/External/HTSLIB/test/c1#pad3.sam
include bsbolt/External/HTSLIB/test/simple_test_driver.sh
include bsbolt/External/HTSLIB/test/c1#unknown.sam
include bsbolt/External/HTSLIB/test/c2.fa.fai
include bsbolt/External/HTSLIB/test/bgziptest.txt.gz.gzi
include bsbolt/External/HTSLIB/test/test-regidx.c
include bsbolt/External/HTSLIB/test/header_syms.pl
include bsbolt/External/HTSLIB/test/sam.c
include bsbolt/External/HTSLIB/test/hts_endian.c
include bsbolt/External/HTSLIB/test/xx#minimal.sam
include bsbolt/External/HTSLIB/test/realn02.fa
include bsbolt/External/HTSLIB/test/test-vcf-sweep.out
include bsbolt/External/HTSLIB/test/fastqs.fq
include bsbolt/External/HTSLIB/test/test_index.c
include bsbolt/External/HTSLIB/test/realn01_exp-e.sam
include bsbolt/External/HTSLIB/test/test.pl
include bsbolt/External/HTSLIB/test/formatcols.vcf
include bsbolt/External/HTSLIB/test/c1.fa.fai
include bsbolt/External/HTSLIB/test/range.bam.bai
include bsbolt/External/HTSLIB/test/realn01.fa.fai
include bsbolt/External/HTSLIB/test/bgziptest.txt
include bsbolt/External/HTSLIB/test/faidx.fa
include bsbolt/External/HTSLIB/test/c2#pad.sam
include bsbolt/External/HTSLIB/test/ce#5b.sam
include bsbolt/External/HTSLIB/test/test_str2int.c
include bsbolt/External/HTSLIB/test/realn02_exp-e.sam
include bsbolt/External/HTSLIB/test/realn02_exp-a.sam
include bsbolt/External/HTSLIB/test/bgziptest.txt.gz
include bsbolt/External/HTSLIB/test/ce#unmap2.sam
include bsbolt/External/HTSLIB/test/ce#supp.sam
include bsbolt/External/HTSLIB/test/index.bam.csi
include bsbolt/External/HTSLIB/test/xx#tlen2.sam
include bsbolt/External/HTSLIB/test/thrash_threads7.c
include bsbolt/External/HTSLIB/test/index.vcf.gz.tbi
include bsbolt/External/HTSLIB/test/test-vcf-api.out
include bsbolt/External/HTSLIB/test/xx#large_aux.sam
include bsbolt/External/HTSLIB/test/auxf.fa.fai
include bsbolt/External/HTSLIB/test/formatmissing-out.vcf
include bsbolt/External/HTSLIB/test/tabix.out
include bsbolt/External/HTSLIB/test/test_kstring.c
include bsbolt/External/HTSLIB/test/xx#MD2.sam
include bsbolt/External/HTSLIB/test/test-vcf-sweep.c
include bsbolt/External/HTSLIB/test/test-vcf-api.c
include bsbolt/External/HTSLIB/test/index.vcf.gz.csi
include bsbolt/External/HTSLIB/test/ce#2.sam
include bsbolt/External/HTSLIB/test/formatmissing.vcf
include bsbolt/External/HTSLIB/test/realn01.fa
include bsbolt/External/HTSLIB/test/xx#MD.sam
include bsbolt/External/HTSLIB/test/ce#1000.sam
include bsbolt/External/HTSLIB/test/cross_validate.sh
include bsbolt/External/HTSLIB/test/thread_pool.md
include bsbolt/External/HTSLIB/test/realn01_exp-a.sam
include bsbolt/External/HTSLIB/test/colons.bam.bai
include bsbolt/External/HTSLIB/test/xx#triplet.sam
include bsbolt/External/HTSLIB/test/xx#unsorted.sam
include bsbolt/External/HTSLIB/test/test_realn.c
include bsbolt/External/HTSLIB/test/index.cram.crai
include bsbolt/External/HTSLIB/test/no_hdr_sq_1.bam
include bsbolt/External/HTSLIB/test/ce#unmap.sam
include bsbolt/External/HTSLIB/test/hts_endian.c
include bsbolt/External/HTSLIB/test/thrash_threads4.c
include bsbolt/External/HTSLIB/test/index.sam
include bsbolt/External/HTSLIB/test/ce#unmap1.sam
include bsbolt/External/HTSLIB/test/noroundtrip-out.vcf
include bsbolt/External/HTSLIB/test/c1#pad2.sam
include bsbolt/External/HTSLIB/test/realn02.sam
include bsbolt/External/HTSLIB/test/ce.fa
include bsbolt/External/HTSLIB/test/xx.fa
include bsbolt/External/HTSLIB/test/test-bcf-sr.c
include bsbolt/External/HTSLIB/test/colons.bam
include bsbolt/External/HTSLIB/test/md#1.sam
include bsbolt/External/HTSLIB/test/c1#bounds.sam
include bsbolt/External/HTSLIB/test/auxf#values_java.cram
include bsbolt/External/HTSLIB/test/c1.fa
include bsbolt/External/HTSLIB/test/thrash_threads2.c
include bsbolt/External/HTSLIB/test/c1#clip.sam
include bsbolt/External/HTSLIB/test/ce#tag_padded.sam
include bsbolt/External/HTSLIB/test/hfile.c
include bsbolt/External/HTSLIB/test/test_view.c
include bsbolt/External/HTSLIB/test/fastqs_README.txt
include bsbolt/External/HTSLIB/test/c1#pad1.sam
include bsbolt/External/HTSLIB/test/no_hdr_sq_1.bam.csi
include bsbolt/External/HTSLIB/test/realn02-r.sam
include bsbolt/External/HTSLIB/test/c2.fa
include bsbolt/External/HTSLIB/test/test-parse-reg.c
include bsbolt/External/HTSLIB/test/range.cram.crai
include bsbolt/External/HTSLIB/test/test-vcf-hdr-in.vcf
include bsbolt/External/HTSLIB/test/range.cram
include bsbolt/External/HTSLIB/test/fieldarith.sam
include bsbolt/External/HTSLIB/test/ce#large_seq.sam
include bsbolt/External/HTSLIB/test/range.out
include bsbolt/External/HTSLIB/test/index.bcf.csi
include bsbolt/External/HTSLIB/test/pileup.c
include bsbolt/External/HTSLIB/test/xx#large_aux2.sam
include bsbolt/External/HTSLIB/test/thrash_threads3.c
include bsbolt/External/HTSLIB/test/index.sam.gz.bai
include bsbolt/External/HTSLIB/test/md.fa.fai
include bsbolt/External/HTSLIB/test/xx#repeated.sam
include bsbolt/External/HTSLIB/test/realn01_exp.sam
include bsbolt/External/HTSLIB/test/ce.fa.fai
include bsbolt/External/HTSLIB/test/auxf#values.sam
include bsbolt/External/HTSLIB/test/thrash_threads5.c
include bsbolt/External/HTSLIB/test/auxf.fa
include bsbolt/External/HTSLIB/test/emptyfile
include bsbolt/External/HTSLIB/test/ce#tag_depadded.sam
include bsbolt/External/HTSLIB/test/c1#noseq.sam
include bsbolt/External/HTSLIB/test/test-bcf-translate.out
include bsbolt/External/HTSLIB/test/ce#5.sam
include bsbolt/External/HTSLIB/test/xx.fa.fai
include bsbolt/External/HTSLIB/test/index.sam.gz.csi
include bsbolt/External/HTSLIB/test/xx#large_aux_java.cram
include bsbolt/External/HTSLIB/test/thrash_threads1.c
include bsbolt/External/HTSLIB/test/range.bam
include bsbolt/External/HTSLIB/test/ce#5b_java.cram
include bsbolt/External/HTSLIB/test/test-vcf-hdr.out
include bsbolt/External/HTSLIB/test/compare_sam.pl
include bsbolt/External/HTSLIB/test/noroundtrip.vcf
include bsbolt/External/HTSLIB/test/realn01.sam
include bsbolt/External/HTSLIB/test/index.vcf
include bsbolt/External/HTSLIB/test/test_bgzf.c
include bsbolt/External/HTSLIB/test/mpileup/c1#pad3.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_I.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_DI.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_P.out
include bsbolt/External/HTSLIB/test/mpileup/mp_D.out
include bsbolt/External/HTSLIB/test/mpileup/mp_D.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_N.out
include bsbolt/External/HTSLIB/test/mpileup/test-pileup.sh
include bsbolt/External/HTSLIB/test/mpileup/c1#pad2.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_N.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_DI.out
include bsbolt/External/HTSLIB/test/mpileup/c1#pad1.sam
include bsbolt/External/HTSLIB/test/mpileup/c1#pad2.out
include bsbolt/External/HTSLIB/test/mpileup/c1#pad1.out
include bsbolt/External/HTSLIB/test/mpileup/small.out
include bsbolt/External/HTSLIB/test/mpileup/mp_I.out
include bsbolt/External/HTSLIB/test/mpileup/c1#pad3.out
include bsbolt/External/HTSLIB/test/mpileup/small.bam
include bsbolt/External/HTSLIB/test/mpileup/mpileup.tst
include bsbolt/External/HTSLIB/test/mpileup/mp_N2.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_N2.out
include bsbolt/External/HTSLIB/test/mpileup/mp_ID.out
include bsbolt/External/HTSLIB/test/mpileup/mp_P.sam
include bsbolt/External/HTSLIB/test/mpileup/mp_ID.sam
include bsbolt/External/HTSLIB/test/fuzz/hts_open_fuzzer.c
include bsbolt/External/HTSLIB/test/tabix/gff_file.X.2934832.2935190.out
include bsbolt/External/HTSLIB/test/tabix/vcf_file.bcf
include bsbolt/External/HTSLIB/test/tabix/gff_file.gff
include bsbolt/External/HTSLIB/test/tabix/bed_file.Y.100200.out
include bsbolt/External/HTSLIB/test/tabix/bed_file.bed
include bsbolt/External/HTSLIB/test/tabix/test-tabix.sh
include bsbolt/External/HTSLIB/test/tabix/tabix.tst
include bsbolt/External/HTSLIB/test/tabix/large_chr.vcf
include bsbolt/External/HTSLIB/test/tabix/large_chr.20.1.2147483647.out
include bsbolt/External/HTSLIB/test/tabix/vcf_file.vcf
include bsbolt/External/HTSLIB/test/tabix/vcf_file.2.3199812.out
include bsbolt/External/HTSLIB/test/tabix/vcf_file.1.3000151.out
include bsbolt/External/HTSLIB/test/longrefs/index.expected2.vcf
include bsbolt/External/HTSLIB/test/longrefs/index.expected1.vcf
include bsbolt/External/HTSLIB/test/longrefs/longref_multi.expected.sam
include bsbolt/External/HTSLIB/test/longrefs/longref_itr.expected.sam
include bsbolt/External/HTSLIB/test/longrefs/longref.sam
include bsbolt/External/HTSLIB/test/longrefs/index.vcf
include bsbolt/External/HTSLIB/test/maintainer/check_spaces.pl
include bsbolt/External/HTSLIB/test/maintainer/check_copyright.pl
include bsbolt/External/HTSLIB/LICENSE