v2.2.2

This is a minor update incorporating a new function in vast-tools secondary modules.

NEW

• compare and tidy have a new option, --noB3, by which exons are filtered out if they contain 0 reads supporting the upstream or downstream inclusion and at least 15 supporting the other. These cases are usually due to alternative first or last exons that in some cases behave as true cassette exons.

• To allow the --noB3 option, the fourth score for alternative exons (excluding those quantified by the microexon pipeline), quantifying the imbalance between inclusion read sets, now includes the B3 score (exons now considered B3 were previously considered B2). In addition, the third and fourth scores of other event types have been modified to provide more meaningful information (specifically, the number exon-exon junction reads). These format changes are silent for all modules, as this information is not used by any module. See README for further information about the scores.

Updates and fixes

• IR files run with IR_version 1 with release v1 or previous were not compatible with the current combine module.