LICENSE
README.md
pyproject.toml
setup.py
taffy/__init__.py
taffy/_taffy_build.py
taffy/lib.py
taffy/ml.py
taffy/newick.py
taffy/wiggle.py
taffy.egg-info/PKG-INFO
taffy.egg-info/SOURCES.txt
taffy.egg-info/dependency_links.txt
taffy.egg-info/requires.txt
taffy.egg-info/top_level.txt
taffy/impl/alignment_block.c
taffy/impl/line_iterator.c
taffy/impl/maf.c
taffy/impl/merge_adjacent_alignments.c
taffy/impl/ond.c
taffy/impl/paf.c
taffy/impl/prefix_sort.c
taffy/impl/taf.c
taffy/impl/tai.c
taffy/impl/wiggle.c
taffy/inc/line_iterator.h
taffy/inc/ond.h
taffy/inc/taf.h
taffy/inc/tai.h
taffy/submodules/abPOA/include/abpoa.h
taffy/submodules/abPOA/include/simd_instruction.h
taffy/submodules/sonLib/C/impl/avl.c
taffy/submodules/sonLib/C/impl/bioioC.c
taffy/submodules/sonLib/C/impl/commonC.c
taffy/submodules/sonLib/C/impl/fastCMaths.c
taffy/submodules/sonLib/C/impl/hashTableC.c
taffy/submodules/sonLib/C/impl/hashTableC_itr.c
taffy/submodules/sonLib/C/impl/jsmn.c
taffy/submodules/sonLib/C/impl/lz4.c
taffy/submodules/sonLib/C/impl/lz4.h
taffy/submodules/sonLib/C/impl/lz4hc.c
taffy/submodules/sonLib/C/impl/lz4hc.h
taffy/submodules/sonLib/C/impl/pairwiseAlignment.c
taffy/submodules/sonLib/C/impl/sonLibCache.c
taffy/submodules/sonLib/C/impl/sonLibCommon.c
taffy/submodules/sonLib/C/impl/sonLibCompression.c
taffy/submodules/sonLib/C/impl/sonLibConnectivity.c
taffy/submodules/sonLib/C/impl/sonLibEulerTour.c
taffy/submodules/sonLib/C/impl/sonLibExcept.c
taffy/submodules/sonLib/C/impl/sonLibFile.c
taffy/submodules/sonLib/C/impl/sonLibGlobalsInternal.h
taffy/submodules/sonLib/C/impl/sonLibHash.c
taffy/submodules/sonLib/C/impl/sonLibKVDatabase.c
taffy/submodules/sonLib/C/impl/sonLibKVDatabaseConf.c
taffy/submodules/sonLib/C/impl/sonLibKVDatabasePrivate.h
taffy/submodules/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c
taffy/submodules/sonLib/C/impl/sonLibKVDatabase_MySql.c
taffy/submodules/sonLib/C/impl/sonLibKVDatabase_Redis.c
taffy/submodules/sonLib/C/impl/sonLibKVDatabase_TokyoCabinet.c
taffy/submodules/sonLib/C/impl/sonLibList.c
taffy/submodules/sonLib/C/impl/sonLibListPrivate.h
taffy/submodules/sonLib/C/impl/sonLibMath.c
taffy/submodules/sonLib/C/impl/sonLibNaiveConnectivity.c
taffy/submodules/sonLib/C/impl/sonLibRandom.c
taffy/submodules/sonLib/C/impl/sonLibSet.c
taffy/submodules/sonLib/C/impl/sonLibSortedSet.c
taffy/submodules/sonLib/C/impl/sonLibString.c
taffy/submodules/sonLib/C/impl/sonLibTreap.c
taffy/submodules/sonLib/C/impl/sonLibTree.c
taffy/submodules/sonLib/C/impl/sonLibTuples.c
taffy/submodules/sonLib/C/impl/stGraph.c
taffy/submodules/sonLib/C/impl/stJson.c
taffy/submodules/sonLib/C/impl/stMatrix.c
taffy/submodules/sonLib/C/impl/stPhylogeny.c
taffy/submodules/sonLib/C/impl/stPosetAlignment.c
taffy/submodules/sonLib/C/impl/stSafeC.c
taffy/submodules/sonLib/C/impl/stThreadPool.c
taffy/submodules/sonLib/C/impl/stUnionFind.c
taffy/submodules/sonLib/C/inc/avl.h
taffy/submodules/sonLib/C/inc/bioioC.h
taffy/submodules/sonLib/C/inc/commonC.h
taffy/submodules/sonLib/C/inc/fastCMaths.h
taffy/submodules/sonLib/C/inc/hashTableC.h
taffy/submodules/sonLib/C/inc/hashTableC_itr.h
taffy/submodules/sonLib/C/inc/hashTablePrivateC.h
taffy/submodules/sonLib/C/inc/jsmn.h
taffy/submodules/sonLib/C/inc/pairwiseAlignment.h
taffy/submodules/sonLib/C/inc/safesort.h
taffy/submodules/sonLib/C/inc/sonLib.h
taffy/submodules/sonLib/C/inc/sonLibCache.h
taffy/submodules/sonLib/C/inc/sonLibCommon.h
taffy/submodules/sonLib/C/inc/sonLibCompression.h
taffy/submodules/sonLib/C/inc/sonLibConnectivity.h
taffy/submodules/sonLib/C/inc/sonLibEulerTour.h
taffy/submodules/sonLib/C/inc/sonLibExcept.h
taffy/submodules/sonLib/C/inc/sonLibFile.h
taffy/submodules/sonLib/C/inc/sonLibHash.h
taffy/submodules/sonLib/C/inc/sonLibKVDatabase.h
taffy/submodules/sonLib/C/inc/sonLibKVDatabaseConf.h
taffy/submodules/sonLib/C/inc/sonLibList.h
taffy/submodules/sonLib/C/inc/sonLibMath.h
taffy/submodules/sonLib/C/inc/sonLibNaiveConnectivity.h
taffy/submodules/sonLib/C/inc/sonLibRandom.h
taffy/submodules/sonLib/C/inc/sonLibSet.h
taffy/submodules/sonLib/C/inc/sonLibSortedSet.h
taffy/submodules/sonLib/C/inc/sonLibString.h
taffy/submodules/sonLib/C/inc/sonLibTreap.h
taffy/submodules/sonLib/C/inc/sonLibTree.h
taffy/submodules/sonLib/C/inc/sonLibTuples.h
taffy/submodules/sonLib/C/inc/sonLibTypes.h
taffy/submodules/sonLib/C/inc/stGraph.h
taffy/submodules/sonLib/C/inc/stJson.h
taffy/submodules/sonLib/C/inc/stMatrix.h
taffy/submodules/sonLib/C/inc/stPhylogeny.h
taffy/submodules/sonLib/C/inc/stPosetAlignment.h
taffy/submodules/sonLib/C/inc/stSafeC.h
taffy/submodules/sonLib/C/inc/stSpimapLayer.h
taffy/submodules/sonLib/C/inc/stThreadPool.h
taffy/submodules/sonLib/C/inc/stUnionFind.h
taffy/submodules/sonLib/externalTools/cutest/CuTest.h