COPYING
INSTALL
KNOWN_BUGS
MANIFEST.in
THANKS
distribute_setup.py
setup.cfg
setup.py
pysam/Pileup.py
pysam/TabProxies.c
pysam/TabProxies.pxd
pysam/TabProxies.pyx
pysam/VCF.py
pysam/__init__.py
pysam/csamtools.c
pysam/csamtools.pxd
pysam/csamtools.pyx
pysam/ctabix.c
pysam/ctabix.pxd
pysam/ctabix.pyx
pysam/cvcf.c
pysam/cvcf.pxd
pysam/cvcf.pyx
pysam/namedtuple.py
pysam/pysam_util.c
pysam/pysam_util.h
pysam/tabix_util.c
pysam/version.py
pysam.egg-info/PKG-INFO
pysam.egg-info/SOURCES.txt
pysam.egg-info/dependency_links.txt
pysam.egg-info/not-zip-safe
pysam.egg-info/requires.txt
pysam.egg-info/top_level.txt
samtools/bam.c.pysam.c
samtools/bam.h
samtools/bam2bcf.c.pysam.c
samtools/bam2bcf.h
samtools/bam2bcf_indel.c.pysam.c
samtools/bam2depth.c.pysam.c
samtools/bam_aux.c.pysam.c
samtools/bam_cat.c.pysam.c
samtools/bam_color.c.pysam.c
samtools/bam_endian.h
samtools/bam_import.c.pysam.c
samtools/bam_index.c.pysam.c
samtools/bam_lpileup.c.pysam.c
samtools/bam_mate.c.pysam.c
samtools/bam_md.c.pysam.c
samtools/bam_pileup.c.pysam.c
samtools/bam_plcmd.c.pysam.c
samtools/bam_reheader.c.pysam.c
samtools/bam_rmdup.c.pysam.c
samtools/bam_rmdupse.c.pysam.c
samtools/bam_sort.c.pysam.c
samtools/bam_stat.c.pysam.c
samtools/bam_tview.c.pysam.c
samtools/bedidx.c.pysam.c
samtools/bgzf.c.pysam.c
samtools/bgzf.h
samtools/cut_target.c.pysam.c
samtools/errmod.c.pysam.c
samtools/errmod.h
samtools/faidx.c.pysam.c
samtools/faidx.h
samtools/kaln.c.pysam.c
samtools/kaln.h
samtools/khash.h
samtools/klist.h
samtools/knetfile.c.pysam.c
samtools/knetfile.h
samtools/kprobaln.c.pysam.c
samtools/kprobaln.h
samtools/kseq.h
samtools/ksort.h
samtools/kstring.c.pysam.c
samtools/kstring.h
samtools/phase.c.pysam.c
samtools/pysam.h
samtools/razf.c.pysam.c
samtools/razf.h
samtools/sam.c.pysam.c
samtools/sam.h
samtools/sam_header.c.pysam.c
samtools/sam_header.h
samtools/sam_view.c.pysam.c
samtools/sample.c.pysam.c
samtools/sample.h
samtools/bcftools/bcf.c.pysam.c
samtools/bcftools/bcf.h
samtools/bcftools/bcf2qcall.c.pysam.c
samtools/bcftools/bcfutils.c.pysam.c
samtools/bcftools/call1.c.pysam.c
samtools/bcftools/em.c.pysam.c
samtools/bcftools/fet.c.pysam.c
samtools/bcftools/index.c.pysam.c
samtools/bcftools/kfunc.c.pysam.c
samtools/bcftools/kmin.c.pysam.c
samtools/bcftools/kmin.h
samtools/bcftools/mut.c.pysam.c
samtools/bcftools/prob1.c.pysam.c
samtools/bcftools/prob1.h
samtools/bcftools/vcf.c.pysam.c
samtools/misc/md5.c.pysam.c
samtools/misc/md5.h
samtools/misc/seqtk.c.pysam.c
samtools/win32/xcurses.h
samtools/win32/zconf.h
samtools/win32/zlib.h
tabix/bam_endian.h
tabix/bedidx.c.pysam.c
tabix/bgzf.c.pysam.c
tabix/bgzf.h
tabix/bgzip.c.pysam.c
tabix/index.c.pysam.c
tabix/khash.h
tabix/knetfile.c.pysam.c
tabix/knetfile.h
tabix/kseq.h
tabix/ksort.h
tabix/kstring.c.pysam.c
tabix/kstring.h
tabix/pysam.h
tabix/tabix.h
tests/00README.txt
tests/Makefile
tests/ex1.fa
tests/ex1.sam.gz
tests/ex10.sam
tests/ex3.sam
tests/ex4.sam
tests/ex5.sam
tests/ex6.sam
tests/ex7.sam
tests/ex8.sam
tests/ex9_fail.bam
tests/ex9_nofail.bam
tests/example.bed.gz
tests/example.bed.gz.tbi
tests/example.gtf.gz
tests/example.gtf.gz.tbi
tests/example.py
tests/example.vcf40
tests/example_btag.sam
tests/example_empty_header.bam
tests/example_unmapped_reads_no_sq.sam
tests/example_user_header.sam
tests/issue100.bam
tests/pysam_test.py
tests/segfault_tests.py
tests/tabix_test.py
tests/tag_bug.bam
tests/vcf-examples/10.vcf
tests/vcf-examples/11.vcf
tests/vcf-examples/12.vcf
tests/vcf-examples/13.vcf
tests/vcf-examples/15.vcf
tests/vcf-examples/16.vcf
tests/vcf-examples/18.vcf
tests/vcf-examples/2.vcf
tests/vcf-examples/20.vcf
tests/vcf-examples/21.vcf
tests/vcf-examples/22.vcf
tests/vcf-examples/23.vcf
tests/vcf-examples/24.vcf
tests/vcf-examples/3.vcf
tests/vcf-examples/4.vcf
tests/vcf-examples/5.vcf
tests/vcf-examples/6.vcf
tests/vcf-examples/7.vcf
tests/vcf-examples/8.vcf
tests/vcf-examples/9.vcf
tests/vcf-examples/issue85.vcf