tiny-count: expanded support for non-collapsed and 3rd-party-collapsed SAM files#217

Merged

taimontgomery merged 17 commits intomasterfrom

Aug 15, 2022

Commits on Apr 7, 2022

Counter now offers basic support for counting SAM files which were not produced by the pipeline. This commit simply changes how sequence counts are determined from each alignment's QNAME field. If …
AlexTate
committed

Commits on Apr 9, 2022

The SAM_reader class has been adapted to handle fastx_collapser QNAME in addition to those made by tiny-collapse. If a SAM file contains fastx style QNAMEs then it is also required that the SAM fil…
AlexTate
committed

Commits on Jul 26, 2022

Commits on Jul 30, 2022

Light refactoring to help clean up SAM_reader
AlexTate
committed

Commits on Jul 31, 2022

Commits on Aug 4, 2022

Commits on Aug 9, 2022

Documentation update to indicate that third party and non-collapsed SAM inputs are now accepted by tiny-count.
AlexTate
committed

Commits on Aug 11, 2022

Expanded on the "non-collapsed SAM file caveats" in tiny-count.md. The description now addresses the effect these files will have on sequence-related stats
AlexTate
committed