MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
doc/Makefile
doc/README.rst
doc/changes.rst
doc/conf.py
doc/develop.rst
doc/faq.rst
doc/guide.rst
doc/howtocite.rst
doc/index.rst
doc/installation.rst
doc/notes.rst
src/backwardcolumniterator.cpp
src/backwardcolumniterator.h
src/columnindexingiterator.cpp
src/columnindexingiterator.h
src/columnindexingscheme.cpp
src/columnindexingscheme.h
src/columniterator.cpp
src/columniterator.h
src/entry.cpp
src/entry.h
src/genotypecolumncostcomputer.cpp
src/genotypecolumncostcomputer.h
src/genotypedistribution.cpp
src/genotypedistribution.h
src/genotypedptable.cpp
src/genotypedptable.h
src/genotyper.cpp
src/genotyper.h
src/graycodes.cpp
src/graycodes.h
src/indexset.cpp
src/indexset.h
src/pedigree.cpp
src/pedigree.h
src/pedigreecolumncostcomputer.cpp
src/pedigreecolumncostcomputer.h
src/pedigreedptable.cpp
src/pedigreedptable.h
src/pedigreepartitions.cpp
src/pedigreepartitions.h
src/phredgenotypelikelihoods.cpp
src/phredgenotypelikelihoods.h
src/read.cpp
src/read.h
src/readset.cpp
src/readset.h
src/transitionprobabilitycomputer.cpp
src/transitionprobabilitycomputer.h
src/vector2d.h
tests/__init__.py
tests/phasingutils.py
tests/test_align.py
tests/test_bam.py
tests/test_genotyping.py
tests/test_graph.py
tests/test_misc.py
tests/test_pedigree.py
tests/test_pedigreegenotyping.py
tests/test_pedigreephasing.py
tests/test_pedreader.py
tests/test_phasing.py
tests/test_priorityqueue.py
tests/test_reads.py
tests/test_readselect.py
tests/test_run_compare.py
tests/test_run_genotype.py
tests/test_run_unphase.py
tests/test_run_whatshap.py
tests/test_utils.py
tests/test_vcf.py
tests/test_verification.py
tests/testvariants.py
whatshap/__init__.py
whatshap/__main__.py
whatshap/_core.cpp
whatshap/_variants.cpp
whatshap/_variants.pyx
whatshap/_version.py
whatshap/align.cpp
whatshap/align.pyx
whatshap/args.py
whatshap/bam.py
whatshap/compare.py
whatshap/core.cpp
whatshap/core.pxd
whatshap/core.pyx
whatshap/coverage.py
whatshap/cpp.pxd
whatshap/genotype.py
whatshap/graph.py
whatshap/hapcut2vcf.py
whatshap/haplotag.py
whatshap/math.py
whatshap/pedigree.py
whatshap/phase.py
whatshap/priorityqueue.cpp
whatshap/priorityqueue.pxd
whatshap/priorityqueue.pyx
whatshap/readselect.pyx
whatshap/stats.py
whatshap/timer.py
whatshap/unphase.py
whatshap/utils.py
whatshap/variants.py
whatshap/vcf.py
whatshap/verification.py
whatshap.egg-info/PKG-INFO
whatshap.egg-info/SOURCES.txt
whatshap.egg-info/dependency_links.txt
whatshap.egg-info/entry_points.txt
whatshap.egg-info/requires.txt
whatshap.egg-info/top_level.txt