b2w rewrite to Python #84
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* [Added] Reads.fas logic * [Added] Minimal docs sphinx * [Updated] CI Docker * [Fixed] CI * [Added] Logic for reads.fas generation
* [Added] Restructered doc and b2w interface * [Added] argparse for b2w * [Changed] Pytest parametrized by different b2w inputs; Old b2w version used to generate test data * [Changed] Restructed testing for more general test sets * [Added] tiling strategy class * [Fixed] tests path * [Added] Additional test data set [Fixed] Numerous bugs in b2w
* [Added] Restructered doc and b2w interface * [Added] argparse for b2w * [Changed] Pytest parametrized by different b2w inputs; Old b2w version used to generate test data * [Changed] Restructed testing for more general test sets * [Added] tiling strategy class * [Fixed] tests path * [Added] Additional test data set [Fixed] Numerous bugs in b2w * [Added] Impl of maximum_reads * [Added] Impl for minimum_reads
* [Added] Cpp bindings [Fixed] Mem leaks in dpm_sampler * [Added] Old b2w with Cpp interface, long_deletion test [Fixed] All tests * [Added] Workflow, [Removed] Examples that were converted to tests * [Fixed] Missing deps * [Fixed] GHA yaml * [Fixed] Upload wheel * [Fixed] tar gz * [Added] Release flow * [Added] Release without tag * [Fix] Use short SHA as tag * [Fix] setuptools * [Fixed] docs [Fixed] Version bump numpy ndarray issue * [Fix] Cleanup files and file names * [Fix] GH file naming convention * [Fix] Release notes * [Fix] CI tagging * [Fix] CI tagging * [Fix] CI restructured * [Fix] CI name * [Add] conda env * [Fix] conda pin versions * [Add] Bump versions [Remove] Dead code __future__ * [Changed] trimer tiling (triple) * [Fix] Tuple vs list issue in tiling * [Fix] Windows for primer tiling * [Add] todos for incomplete code refactoring * [Draft] shorah snv rewrite to more flexible windows * [Removed] Release action because pip allows installs from branch * [Added] Shorah shotgun -r is now optional * [Fixed] Without region flag -r
* [Removed] amplicon mode * [Added] Cleanup of shorah_snv with new csv format * [Fixed] Output files and their location * [Fixed] New output file * [Fixed] Test except for long_del * [Fixed] Long deletion test
* [Added] Also output fas for each window * [Fixed] Unit tests * [Added] Conformance flag to old version, resolved issue
* [Added] Also output fas for each window * [Fixed] Unit tests * [Added] Conformance flag to old version, resolved issue * [Added] Improved docs
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[Added]
b2w.cppto Python utilizingpysam[Removed]
b2w.cpp[Fixed]
reads.fasBreaking changes in
b2w.pyvsb2w.cpp-doption not longer availableregionnot longer optional