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Initial implementation of bwapy#1

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nh13 wants to merge 50 commits intomainfulcrumgenomics/pybwa:mainfrom feat/initfulcrumgenomics/pybwa:feat/initCopy head branch name to clipboard

+61,938-1

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Commits on Dec 16, 2024

• feat: initial implementation of python bindings for bwa aln

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• fix

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Commits on Dec 17, 2024

• Split bwa aln and bwa index into multiple

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Commits on Dec 18, 2024

• start on bwa mem bindings

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• wip

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• bwamem

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• fixes

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• fix again

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Commits on Dec 19, 2024

• refactoring bwa options

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• fixes

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• fixups

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• fix

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• docs

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• strict

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• updating some build stuff

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• Adding in bwa aln additional tags

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• adding bwa mem tags except SA

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• Add support for SA tag in bwa mem

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• debug

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• renaming to pybwa

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• fixes

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• fixes

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• fixes

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• rtd yaml

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Commits on Jan 7, 2025

• bug fix: query qualities

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Commits on Jan 8, 2025

• updates

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• fixes

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• a bit more

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• fixes to bwa mem

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Commits on Jan 9, 2025

• use sphinx

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• add

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• fixup

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• fix rtd yml

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• rtd fixups

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• doc fixups

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• add console

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• fix link shortening

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• updates

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• more

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• add code to inline

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• fix up some api links and code blocks

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• fix

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• attempts at type hints

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Commits on Jan 10, 2025

• Update api.rst

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• Update api.rst

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Commits on Jan 13, 2025

• alternative to BwaMemOptions (#3)

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• Update README.md

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Commits on Jan 14, 2025

• review fixups

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• add bwa as a submodule

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• use https

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