tiny-count: support for sequence-based read counting#279

Merged

taimontgomery merged 22 commits intomasterfrom

Feb 7, 2023

Commits on Jan 27, 2023

Updating PathsFile class to no longer treat gff_files as required, and to skip empty paths under the gff_files key
AlexTate
committed
Minor refactor to match the order of enumerate()'s (index, element) outputs since this code is essentially an enumerate() with an upper limit
AlexTate
committed
Updating tiny-count's load_gff_files() to treat GFF files as optional
AlexTate
committed
Updating SAM_reader to properly store header data when multiple header lines start with the same flag
AlexTate
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Refactoring ReferenceTables to use a base class for functionality that is shared between it and the new class for non-genomic references. The overlap between the two is pretty much the GenomicArray…
AlexTate
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Adding a new class that is essentially the equivalent of ReferenceTables but for non-GFF read counting. It produces a GenomicArray of reference sequences, where there is one "chromosome" for each s…
AlexTate
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Updating FeatureCounter to switch between the two reference annotation classes based on the presence of GFF files. Also changing the order in which assign_features and count_reads occur in the clas…
AlexTate
committed

Commits on Feb 4, 2023

Commits on Feb 7, 2023

Adding a timeout to the sequence-based counting notice that is issued when users don't have GFF files listed.
AlexTate
committed