0.31.1 - 2024-01-31

Added

• Fixed package level doc strings for search and bwt packages.

[0.31.0] - 2024-01-31

Added

• Basic BWT for sub-sequence count and offset for sequence alignment. Only supports exact matches for now.
• Moved BWT, align, and mash packages to new search sub-directory.
• Implemented Run-Length Burrows Wheeler Transform.

This is just a placeholder until the nightly release bot kicks in.

Changelog

• 05cdd6d migrated namespace from TimothyStiles/poly to bebop/poly
• 8ea0d04 patched start codon regression (#414)
• f76bf05 fixed bug where linear, non-directional, single cuts were copying and not just moving overhangs from the fragment sequence. (#409)
• d0f6ab3 fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. (#408)

Changelog

• 165561e fixed bug where linear, non-directional, single cuts were copying and not just moving overhangs from the fragment sequence.
• d0f6ab3 fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. (#408)

Changelog

• 93e89eb fixed bug that produced wrong overhang in linear, non-directional, single cut reactions.

Changelog

• 916c92d renamed OptimizeSequence to just Optimize. (#407)

Changelog

• c9ba7f3 added example test for mash usage. (#404)
• 489cf97 Add FragmentWithOverhangs (#387)
• 96b5cff Add stats to codon tables (#350)
• e96a63e Cloning refactor and data race fix (#393)
• 58f8699 mash: optimize mash similarity function, add benchmark (#395)

Added

Alternative start codons can now be used in the synthesis/codon DNA -> protein translation package (#305)
Added a parser and writer for the pileup sequence alignment format (#329)
Added statistics to the synthesis/codon package (keeping track of the observed start codon occurrences in a translation table) (#350)
Added option to fragmenter to fragment with only certain overhangs (#387)

Fixed

fastq parser no longer becomes de-aligned when reading (#325)
fastq now handles optionals correctly (#323)
No more data race in GoldenGate (#276)

Breaking

CutWithEnzymeByName is now a receiver of EnzymeManager. GoldenGate now takes an Enzyme instead of the name of an enzyme. This is an effort to remove dependence on some package level global state and build some flexibility managing enzymes over the lifetime of the program.
Enzyme.OverhangLen is now named Enzyme.OverhangLength

Tim just discovered some codon optimization API breakage... -_-

Changelog

• 2d5d8c4 patched genbank parser and builder to handle BASE COUNT. (#386)
• f2310db created parser regression test for nested sublocations. (#385)

Changelog

• 5bd6a5d fixed mash.NewMash to mash.New.