tiny-count: new selector: Mismatches#298

Merged

taimontgomery merged 21 commits intomasterfrom

Apr 7, 2023

Commits on Mar 24, 2023

The SAM_reader class now uses pysam for the initial parsing step. The SamSqValidator class has been updated accordingly.
AlexTate
committed

Commits on Mar 31, 2023

Adding some optimizations to the pure-python implementation of _parse_alignments(). It's better but not quite enough. Need to move this function into Cython space for any further gains
AlexTate
committed
The _parse_alignments() method of SAM_reader has been replaced by a dedicated Cython extension class. The extension acts as an iterable over pysam alignments that have been converted to dictionary …
AlexTate
committed
The Mismatches selector has been added to tiny-count, the CSVReacer, and the Features Sheet. An additional class has not been added to matching.py for this selector because it is most efficiently a…
AlexTate
committed

Commits on Apr 3, 2023

Commits on Apr 4, 2023

Bugfixes for decollapsed outputs and sequence-based counting mode
AlexTate
committed

Commits on Apr 5, 2023