MANIFEST.in
README.md
setup.py
PloidPy/__init__.py
PloidPy/binom_model.py
PloidPy/nbinom.py
PloidPy/parse_bam.c
PloidPy/parse_bam.h
PloidPy/ploidy_model.py
PloidPy/plot_read_data.py
PloidPy/process_bam.c
PloidPy/process_bam.pxd
PloidPy/process_bam.pyx
PloidPy.egg-info/PKG-INFO
PloidPy.egg-info/SOURCES.txt
PloidPy.egg-info/dependency_links.txt
PloidPy.egg-info/requires.txt
PloidPy.egg-info/top_level.txt
htslib/.appveyor.yml
htslib/.git
htslib/.gitattributes
htslib/.gitignore
htslib/.travis.yml
htslib/INSTALL
htslib/LICENSE
htslib/Makefile
htslib/NEWS
htslib/README
htslib/README.large_positions.md
htslib/README.md
htslib/aclocal.m4
htslib/bcf_sr_sort.c
htslib/bcf_sr_sort.h
htslib/bgzf.c
htslib/bgzip.1
htslib/bgzip.c
htslib/config.mk.in
htslib/configure.ac
htslib/errmod.c
htslib/faidx.5
htslib/faidx.c
htslib/header.c
htslib/header.h
htslib/hfile.c
htslib/hfile_gcs.c
htslib/hfile_internal.h
htslib/hfile_libcurl.c
htslib/hfile_net.c
htslib/hfile_s3.c
htslib/hfile_s3_write.c
htslib/hts.c
htslib/hts_internal.h
htslib/hts_os.c
htslib/htsfile.1
htslib/htsfile.c
htslib/htslib-s3-plugin.7
htslib/htslib.mk
htslib/htslib.pc.in
htslib/htslib_vars.mk
htslib/kfunc.c
htslib/knetfile.c
htslib/kstring.c
htslib/md5.c
htslib/multipart.c
htslib/plugin.c
htslib/probaln.c
htslib/realn.c
htslib/regidx.c
htslib/region.c
htslib/sam.5
htslib/sam.c
htslib/sam_internal.h
htslib/synced_bcf_reader.c
htslib/tabix.1
htslib/tabix.c
htslib/tbx.c
htslib/textutils.c
htslib/textutils_internal.h
htslib/thread_pool.c
htslib/thread_pool_internal.h
htslib/vcf.5
htslib/vcf.c
htslib/vcf_sweep.c
htslib/vcfutils.c
htslib/version.sh
htslib/cram/cram.h
htslib/cram/cram_codecs.c
htslib/cram/cram_codecs.h
htslib/cram/cram_decode.c
htslib/cram/cram_decode.h
htslib/cram/cram_encode.c
htslib/cram/cram_encode.h
htslib/cram/cram_external.c
htslib/cram/cram_index.c
htslib/cram/cram_index.h
htslib/cram/cram_io.c
htslib/cram/cram_io.h
htslib/cram/cram_samtools.c
htslib/cram/cram_samtools.h
htslib/cram/cram_stats.c
htslib/cram/cram_stats.h
htslib/cram/cram_structs.h
htslib/cram/mFILE.c
htslib/cram/mFILE.h
htslib/cram/misc.h
htslib/cram/open_trace_file.c
htslib/cram/open_trace_file.h
htslib/cram/os.h
htslib/cram/pooled_alloc.c
htslib/cram/pooled_alloc.h
htslib/cram/rANS_byte.h
htslib/cram/rANS_static.c
htslib/cram/rANS_static.h
htslib/cram/string_alloc.c
htslib/cram/string_alloc.h
htslib/htslib/bgzf.h
htslib/htslib/cram.h
htslib/htslib/faidx.h
htslib/htslib/hfile.h
htslib/htslib/hts.h
htslib/htslib/hts_defs.h
htslib/htslib/hts_endian.h
htslib/htslib/hts_log.h
htslib/htslib/hts_os.h
htslib/htslib/kbitset.h
htslib/htslib/kfunc.h
htslib/htslib/khash.h
htslib/htslib/khash_str2int.h
htslib/htslib/klist.h
htslib/htslib/knetfile.h
htslib/htslib/kroundup.h
htslib/htslib/kseq.h
htslib/htslib/ksort.h
htslib/htslib/kstring.h
htslib/htslib/regidx.h
htslib/htslib/sam.h
htslib/htslib/synced_bcf_reader.h
htslib/htslib/tbx.h
htslib/htslib/thread_pool.h
htslib/htslib/vcf.h
htslib/htslib/vcf_sweep.h
htslib/htslib/vcfutils.h
htslib/m4/hts_hide_dynamic_syms.m4
htslib/m4/hts_prog_cc_warnings.m4
htslib/os/lzma_stub.h
htslib/os/rand.c
htslib/test/auxf#values.sam
htslib/test/auxf#values_java.cram
htslib/test/auxf.fa
htslib/test/auxf.fa.fai
htslib/test/bgziptest.txt
htslib/test/bgziptest.txt.gz
htslib/test/bgziptest.txt.gz.gzi
htslib/test/c1#bounds.sam
htslib/test/c1#clip.sam
htslib/test/c1#noseq.sam
htslib/test/c1#pad1.sam
htslib/test/c1#pad2.sam
htslib/test/c1#pad3.sam
htslib/test/c1#unknown.sam
htslib/test/c1.fa
htslib/test/c1.fa.fai
htslib/test/c2#pad.sam
htslib/test/c2.fa
htslib/test/c2.fa.fai
htslib/test/ce#1.sam
htslib/test/ce#1000.sam
htslib/test/ce#2.sam
htslib/test/ce#5.sam
htslib/test/ce#5b.sam
htslib/test/ce#5b_java.cram
htslib/test/ce#large_seq.sam
htslib/test/ce#supp.sam
htslib/test/ce#tag_depadded.sam
htslib/test/ce#tag_padded.sam
htslib/test/ce#unmap.sam
htslib/test/ce#unmap1.sam
htslib/test/ce#unmap2.sam
htslib/test/ce.fa
htslib/test/ce.fa.fai
htslib/test/colons.bam
htslib/test/colons.bam.bai
htslib/test/compare_sam.pl
htslib/test/cross_validate.sh
htslib/test/emptyfile
htslib/test/faidx.fa
htslib/test/fastqs.fq
htslib/test/fastqs_README.txt
htslib/test/fieldarith.c
htslib/test/fieldarith.sam
htslib/test/formatcols.vcf
htslib/test/formatmissing-out.vcf
htslib/test/formatmissing.vcf
htslib/test/header_syms.pl
htslib/test/hfile.c
htslib/test/hts_endian.c
htslib/test/index.bam.bai
htslib/test/index.bam.csi
htslib/test/index.bcf.csi
htslib/test/index.cram.crai
htslib/test/index.sam
htslib/test/index.sam.gz.bai
htslib/test/index.sam.gz.csi
htslib/test/index.vcf
htslib/test/index.vcf.gz.csi
htslib/test/index.vcf.gz.tbi
htslib/test/md#1.sam
htslib/test/md.fa
htslib/test/md.fa.fai
htslib/test/no_hdr_sq_1.bam
htslib/test/no_hdr_sq_1.bam.csi
htslib/test/no_hdr_sq_1.expected.sam
htslib/test/noroundtrip-out.vcf
htslib/test/noroundtrip.vcf
htslib/test/pileup.c
htslib/test/range.bam
htslib/test/range.bam.bai
htslib/test/range.cram
htslib/test/range.cram.crai
htslib/test/range.out
htslib/test/realn01.fa
htslib/test/realn01.fa.fai
htslib/test/realn01.sam
htslib/test/realn01_exp-a.sam
htslib/test/realn01_exp-e.sam
htslib/test/realn01_exp.sam
htslib/test/realn02-r.sam
htslib/test/realn02.fa
htslib/test/realn02.fa.fai
htslib/test/realn02.sam
htslib/test/realn02_exp-a.sam
htslib/test/realn02_exp-e.sam
htslib/test/realn02_exp.sam
htslib/test/sam.c
htslib/test/simple_test_driver.sh
htslib/test/tabix.out
htslib/test/test-bcf-sr.c
htslib/test/test-bcf-sr.pl
htslib/test/test-bcf-translate.c
htslib/test/test-bcf-translate.out
htslib/test/test-logging.pl
htslib/test/test-parse-reg.c
htslib/test/test-regidx.c
htslib/test/test-vcf-api.c
htslib/test/test-vcf-api.out
htslib/test/test-vcf-hdr-in.vcf
htslib/test/test-vcf-hdr.out
htslib/test/test-vcf-sweep.c
htslib/test/test-vcf-sweep.out
htslib/test/test.pl
htslib/test/test_bgzf.c
htslib/test/test_index.c
htslib/test/test_kstring.c
htslib/test/test_realn.c
htslib/test/test_str2int.c
htslib/test/test_view.c
htslib/test/thrash_threads1.c
htslib/test/thrash_threads2.c
htslib/test/thrash_threads3.c
htslib/test/thrash_threads4.c
htslib/test/thrash_threads5.c
htslib/test/thrash_threads6.c
htslib/test/thrash_threads7.c
htslib/test/thread_pool.md
htslib/test/xx#MD.sam
htslib/test/xx#MD2.sam
htslib/test/xx#blank.sam
htslib/test/xx#large_aux.sam
htslib/test/xx#large_aux2.sam
htslib/test/xx#large_aux_java.cram
htslib/test/xx#minimal.sam
htslib/test/xx#pair.sam
htslib/test/xx#repeated.sam
htslib/test/xx#rg.sam
htslib/test/xx#tlen.sam
htslib/test/xx#tlen2.sam
htslib/test/xx#triplet.sam
htslib/test/xx#unsorted.sam
htslib/test/xx.fa
htslib/test/xx.fa.fai
htslib/test/fuzz/hts_open_fuzzer.c
htslib/test/longrefs/index.expected1.vcf
htslib/test/longrefs/index.expected2.vcf
htslib/test/longrefs/index.vcf
htslib/test/longrefs/longref.sam
htslib/test/longrefs/longref_itr.expected.sam
htslib/test/longrefs/longref_multi.expected.sam
htslib/test/maintainer/check_copyright.pl
htslib/test/maintainer/check_spaces.pl
htslib/test/mpileup/c1#pad1.out
htslib/test/mpileup/c1#pad1.sam
htslib/test/mpileup/c1#pad2.out
htslib/test/mpileup/c1#pad2.sam
htslib/test/mpileup/c1#pad3.out
htslib/test/mpileup/c1#pad3.sam
htslib/test/mpileup/mp_D.out
htslib/test/mpileup/mp_D.sam
htslib/test/mpileup/mp_DI.out
htslib/test/mpileup/mp_DI.sam
htslib/test/mpileup/mp_I.out
htslib/test/mpileup/mp_I.sam
htslib/test/mpileup/mp_ID.out
htslib/test/mpileup/mp_ID.sam
htslib/test/mpileup/mp_N.out
htslib/test/mpileup/mp_N.sam
htslib/test/mpileup/mp_N2.out
htslib/test/mpileup/mp_N2.sam
htslib/test/mpileup/mp_P.out
htslib/test/mpileup/mp_P.sam
htslib/test/mpileup/mpileup.tst
htslib/test/mpileup/small.bam
htslib/test/mpileup/small.out
htslib/test/mpileup/test-pileup.sh
htslib/test/tabix/bed_file.Y.100200.out
htslib/test/tabix/bed_file.bed
htslib/test/tabix/gff_file.X.2934832.2935190.out
htslib/test/tabix/gff_file.gff
htslib/test/tabix/large_chr.20.1.2147483647.out
htslib/test/tabix/large_chr.vcf
htslib/test/tabix/tabix.tst
htslib/test/tabix/test-tabix.sh
htslib/test/tabix/vcf_file.1.3000151.out
htslib/test/tabix/vcf_file.2.3199812.out
htslib/test/tabix/vcf_file.bcf
htslib/test/tabix/vcf_file.vcf
scripts/PloidPy