.editorconfig
.gitignore
.readthedocs.yaml
CHANGES.rst
CITATION.rst
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
tox.ini
.github/issue_template.md
.github/workflows/ci.yml
.github/workflows/macos.yml
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
doc/_static/gtf.png
doc/_static/haplotagged-HP.png
doc/_static/haplotagged-PS.png
logo/Makefile
logo/README.md
logo/whatshap_logo.pdf
logo/whatshap_logo.png
logo/whatshap_logo.svg
logo/whatshap_logo_notext.png
logo/whatshap_logo_notext.svg
logo/whatshap_logo_text.svg
misc/example.py
src/backwardcolumniterator.cpp
src/backwardcolumniterator.h
src/binomial.cpp
src/binomial.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/genotype.cpp
src/genotype.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
src/hapchat/balancedcombinations.cpp
src/hapchat/balancedcombinations.h
src/hapchat/basictypes.cpp
src/hapchat/basictypes.h
src/hapchat/binomialcoefficient.cpp
src/hapchat/binomialcoefficient.h
src/hapchat/combinations.h
src/hapchat/hapchatcolumniterator.cpp
src/hapchat/hapchatcore.cpp
src/hapchat/log.h
src/polyphase/clustereditingsolution.cpp
src/polyphase/clustereditingsolution.h
src/polyphase/clustereditingsolver.cpp
src/polyphase/clustereditingsolver.h
src/polyphase/edgeheap.cpp
src/polyphase/edgeheap.h
src/polyphase/haplothreader.cpp
src/polyphase/haplothreader.h
src/polyphase/inducedcostheuristic.cpp
src/polyphase/inducedcostheuristic.h
src/polyphase/readscoring.cpp
src/polyphase/readscoring.h
src/polyphase/staticsparsegraph.cpp
src/polyphase/staticsparsegraph.h
src/polyphase/switchflipcalculator.cpp
src/polyphase/switchflipcalculator.h
src/polyphase/trianglesparsematrix.cpp
src/polyphase/trianglesparsematrix.h
src/polyphase/tuple.h
src/polyphase/tupleconverter.cpp
src/polyphase/tupleconverter.h
src/testing/CMakeLists.txt
src/testing/catch.hpp
src/testing/test.cpp
tests/test.matrix
tests/test_align.py
tests/test_bam.py
tests/test_clusterediting.py
tests/test_geneticmap.py
tests/test_genotyping.py
tests/test_graph.py
tests/test_main.py
tests/test_merge_reads.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_readscoring.py
tests/test_readselect.py
tests/test_readsetreader.py
tests/test_run_compare.py
tests/test_run_find_snv_candidates.py
tests/test_run_genotype.py
tests/test_run_hapcut2vcf.py
tests/test_run_haplotag.py
tests/test_run_phase.py
tests/test_run_polyphase.py
tests/test_run_split.py
tests/test_run_stats.py
tests/test_run_unphase.py
tests/test_threading.py
tests/test_utils.py
tests/test_vcf.py
tests/test_verification.py
tests/data/chr-lengths.txt
tests/data/duplicate-positions.vcf
tests/data/empty_format.vcf
tests/data/expected-calls.vcf
tests/data/genetic-haplotyping.ped
tests/data/genetic-haplotyping.vcf
tests/data/genotype-likelihoods.vcf
tests/data/haplotag.10X.bam
tests/data/haplotag.10X.bam.bai
tests/data/haplotag.10X.vcf.gz
tests/data/haplotag.10X.vcf.gz.tbi
tests/data/haplotag.10X_2.vcf.gz
tests/data/haplotag.10X_2.vcf.gz.tbi
tests/data/haplotag.10X_3.bam
tests/data/haplotag.10X_3.bam.bai
tests/data/haplotag.bam
tests/data/haplotag.bam.bai
tests/data/haplotag.large.2.vcf.gz
tests/data/haplotag.large.2.vcf.gz.tbi
tests/data/haplotag.large.bam
tests/data/haplotag.large.bam.bai
tests/data/haplotag.large.vcf.gz
tests/data/haplotag.large.vcf.gz.tbi
tests/data/haplotag.missing_chr.vcf.gz
tests/data/haplotag.missing_chr.vcf.gz.tbi
tests/data/haplotag.supplementary.bam
tests/data/haplotag.supplementary.bam.bai
tests/data/haplotag.supplementary.vcf.gz
tests/data/haplotag.supplementary.vcf.gz.tbi
tests/data/haplotag.without_chr2.vcf.gz
tests/data/haplotag.without_chr2.vcf.gz.csi
tests/data/haplotag_1.vcf.gz
tests/data/haplotag_1.vcf.gz.tbi
tests/data/haplotag_2.bcf
tests/data/haplotag_2.bcf.csi
tests/data/haplotag_2.vcf.gz
tests/data/haplotag_2.vcf.gz.tbi
tests/data/haplotag_noRG.bam
tests/data/haplotag_noRG.bam.bai
tests/data/haplotag_noRG.vcf.gz
tests/data/haplotag_noRG.vcf.gz.tbi
tests/data/haplotag_noSM.bam
tests/data/haplotag_noSM.bam.bai
tests/data/haplotag_sample.bam
tests/data/haplotag_sample.bam.bai
tests/data/haplotag_sample.vcf.gz
tests/data/haplotag_sample.vcf.gz.tbi
tests/data/haplotag_with_csi_index.vcf.gz
tests/data/haplotag_with_csi_index.vcf.gz.csi
tests/data/hexadecaploid.chr22.vcf
tests/data/indels.sam
tests/data/indels.vcf
tests/data/missing-headers.vcf
tests/data/multiallelic.vcf
tests/data/multisample.vcf
tests/data/no-readgroup.bam
tests/data/no-readgroup.bam.bai
tests/data/not-indexed.bam
tests/data/not-indexed.fasta
tests/data/oneread-readgroup-without-sample.bam
tests/data/oneread-readgroup-without-sample.bam.bai
tests/data/oneread-ref.fasta
tests/data/oneread-ref.fasta.fai
tests/data/oneread.bam
tests/data/oneread.bam.bai
tests/data/oneread.crai
tests/data/oneread.cram
tests/data/onevariant.vcf
tests/data/onevariant.vcf.gz
tests/data/paired_end.sorted.sam
tests/data/paired_end.sorted.vcf
tests/data/ped_samples.bam
tests/data/ped_samples.bam.bai
tests/data/ped_samples.vcf
tests/data/pedigree.ped
tests/data/phased-blocks.blocks.vcf
tests/data/phased-blocks.reads.bam
tests/data/phased-blocks.reads.bam.bai
tests/data/phased-blocks.variants.vcf
tests/data/phased-via-HP.vcf
tests/data/phased-via-PS.vcf
tests/data/phased-via-mixed-HP-PS.vcf
tests/data/phased.poly1.vcf
tests/data/phased.poly2.vcf
tests/data/phased.poly3.vcf
tests/data/phased1.vcf
tests/data/phased2.vcf
tests/data/phased3.vcf
tests/data/phased_overlapping.vcf
tests/data/phased_single_sample1.vcf
tests/data/phased_single_sample2.vcf
tests/data/phasedinput.vcf
tests/data/polyploid.chr22.42M.12k.bam
tests/data/polyploid.chr22.42M.12k.bam.bai
tests/data/polyploid.chr22.42M.12k.vcf
tests/data/polyploid.chr22.inconsistent.vcf
tests/data/polyploid.chr22.phased.vcf
tests/data/polyploid.chr22.unphased.vcf
tests/data/polyploid.human1.chr22.42M.5k.bam
tests/data/polyploid.human1.chr22.42M.5k.bam.bai
tests/data/polyploid.human2.chr22.42M.5k.bam
tests/data/polyploid.human2.chr22.42M.5k.bam.bai
tests/data/polyploid.multisample.chr22.42M.5k.vcf
tests/data/quartet.vcf.gz
tests/data/quartet.vcf.gz.tbi
tests/data/quartet2.ped
tests/data/quartet2.sam
tests/data/quartet2.vcf
tests/data/random0.fasta
tests/data/random0.fasta.fai
tests/data/reads-no-sequence.bam
tests/data/reads-no-sequence.bam.bai
tests/data/reads-no-sequence.haplotags.tsv
tests/data/recombination_breaks.map
tests/data/recombination_breaks.ped
tests/data/recombination_breaks.sorted.sam
tests/data/string_typed_ps_tag.vcf
tests/data/test_dist_geno.sam
tests/data/test_dist_geno.vcf
tests/data/trio-mendelian-conflict.vcf
tests/data/trio-merged-blocks.sam
tests/data/trio-merged-blocks.vcf
tests/data/trio-missing-genotypes.vcf
tests/data/trio-symbolic-alt.vcf
tests/data/trio-two-chromosomes.vcf
tests/data/trio.map
tests/data/trio.pacbio.sam
tests/data/trio.ped
tests/data/trio.vcf
tests/data/trio_genotype_likelihoods.vcf
tests/data/trio_genotype_log_likelihoods.vcf
tests/data/trio_paired_end.ped
tests/data/unknown-genotype.vcf
tests/data/unmapped.bam
tests/data/unmapped.bam.bai
tests/data/unphased.vcf
tests/data/zero-genetic-distance.map
tests/data/pacbio/.gitignore
tests/data/pacbio/Makefile
tests/data/pacbio/hapcut.txt
tests/data/pacbio/haplotags.txt
tests/data/pacbio/pacbio.bam
tests/data/pacbio/pacbio.bam.bai
tests/data/pacbio/pacbio.crai
tests/data/pacbio/pacbio.cram
tests/data/pacbio/phased.vcf
tests/data/pacbio/phased.vcf.gz
tests/data/pacbio/phased.vcf.gz.tbi
tests/data/pacbio/phased_hapchat.vcf
tests/data/pacbio/reference.fasta
tests/data/pacbio/reference.fasta.fai
tests/data/pacbio/variants.vcf
tests/data/short-genome/.gitignore
tests/data/short-genome/short-hap1.fasta
tests/data/short-genome/short-hap2.fasta
tests/data/short-genome/short-one-read-duplicate.sam
tests/data/short-genome/short-reads.fasta
tests/data/short-genome/short-ref.fasta
tests/data/short-genome/short.sam
tests/data/short-genome/short.vcf
tests/data/short-genome/wrongchromosome.vcf
whatshap/.gitignore
whatshap/__init__.py
whatshap/__main__.py
whatshap/_variants.cpp
whatshap/_variants.pyi
whatshap/_variants.pyx
whatshap/_version.py
whatshap/align.cpp
whatshap/align.pyi
whatshap/align.pyx
whatshap/args.py
whatshap/bam.py
whatshap/core.cpp
whatshap/core.pxd
whatshap/core.pyi
whatshap/core.pyx
whatshap/coverage.py
whatshap/cpp.pxd
whatshap/graph.py
whatshap/merge.py
whatshap/pedigree.py
whatshap/polyphase_solver.cpp
whatshap/polyphase_solver.pxd
whatshap/polyphase_solver.pyi
whatshap/polyphase_solver.pyx
whatshap/polyphaseplots.py
whatshap/polyphaseutil.py
whatshap/priorityqueue.cpp
whatshap/priorityqueue.pxd
whatshap/priorityqueue.pyi
whatshap/priorityqueue.pyx
whatshap/readselect.cpp
whatshap/readselect.pyi
whatshap/readselect.pyx
whatshap/reorder.py
whatshap/testhelpers.py
whatshap/threading.py
whatshap/timer.py
whatshap/utils.py
whatshap/variant.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
whatshap/cli/__init__.py
whatshap/cli/compare.py
whatshap/cli/find_snv_candidates.py
whatshap/cli/genotype.py
whatshap/cli/hapcut2vcf.py
whatshap/cli/haplotag.py
whatshap/cli/phase.py
whatshap/cli/polyphase.py
whatshap/cli/split.py
whatshap/cli/stats.py
whatshap/cli/unphase.py