MANIFEST.in
README.rst
setup.cfg
setup.py
versioneer.py
bin/_preamble.py
bin/whatshap
doc/Makefile
doc/changes.rst
doc/conf.py
doc/develop.rst
doc/faq.rst
doc/guide.rst
doc/index.rst
doc/installation.rst
doc/notes.rst
src/columncostcomputer.cpp
src/columncostcomputer.h
src/columnindexingiterator.cpp
src/columnindexingiterator.h
src/columnindexingscheme.cpp
src/columnindexingscheme.h
src/columniterator.cpp
src/columniterator.h
src/dptable.cpp
src/dptable.h
src/entry.cpp
src/entry.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/read.cpp
src/read.h
src/readset.cpp
src/readset.h
src/vector2d.h
tests/__init__.py
tests/phasingutils.py
tests/testalign.py
tests/testbam.py
tests/testgraph.py
tests/testmain.py
tests/testpedigreephasing.py
tests/testpedreader.py
tests/testphasing.py
tests/testpriorityqueue.py
tests/testreads.py
tests/testreadselect.py
tests/tests.py
tests/testunphase.py
tests/testvcf.py
tests/testverification.py
whatshap/__init__.py
whatshap/__main__.py
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/example.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/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