MANIFEST.in
README.rst
setup.py
bin/_preamble.py
bin/phasingstats
bin/whatshap
doc/Makefile
doc/conf.py
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/read.cpp
src/read.h
src/readset.cpp
src/readset.h
tests/__init__.py
tests/phasingutils.py
tests/testbam.py
tests/testcore.py
tests/testpriorityqueue.py
tests/testreadselect.py
tests/tests.py
tests/testvcf.py
whatshap/__init__.py
whatshap/_core.cpp
whatshap/_core.pyx
whatshap/args.py
whatshap/bam.py
whatshap/core.py
whatshap/coverage.py
whatshap/cppwrapper.pyx
whatshap/graph.py
whatshap/priorityqueue.pyx
whatshap/readselect.pyx
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/requires.txt
whatshap.egg-info/top_level.txt
whatshap/scripts/__init__.py
whatshap/scripts/phasingstats.py
whatshap/scripts/whatshap.py