IsoQuant Files

Optimized grouped counts output. By default, all counts are stored in linear format, which saves time and disk space. Matrices with small number of columns are automatically converted to usual matrix in TSV format, larger matrices typical for single-cell and spatial data are converted to MTX format. See --counts_format paramter for options. It is also possible to convert counts after IsoQuant is finished using src/convert_grouped_counts.py. Fixes issues mentioned in https://github.com/ablab/IsoQuant/issues/248

Renamed counts related to discovered transcripts and genes to avoid confusion.

New options --indexing_options and --mapping_options that allow to pass options to the indexing and mapping commands. Fixes https://github.com/ablab/IsoQuant/issues/284 and https://github.com/ablab/IsoQuant/issues/259

STARlong is now an alternative options for aligning, can be set via --aligner starlong (not recommended for ONT reads). Fixes https://github.com/ablab/IsoQuant/issues/284

Exon/splice junction counts now only come from reads assigned to the same strand, fixes https://github.com/ablab/IsoQuant/issues/253

Use only gene-assigned reads for exon counting, fixes https://github.com/ablab/IsoQuant/issues/283

Fixed rare serialization bug https://github.com/ablab/IsoQuant/issues/304