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Major changes are:
Added SV annotation using AnnotSV
- in addition to default genomecomb annotation
- option -extraannot AnnotSV
isoquant use
- fixed important bug in merging known and novel transcripts that could caused novel transcript counts to be overinflated sometimes
clair3 variant analysis
- new version 1.1.1
- now select model based on basecaller version info in the bam/cram (if available)
Added functionality
- cg select - added function exonlist
- cg mm2tsv (wip)
- cg tsv2mm (wip)
- cg var_apply (wip)
Full Changelog: 0.111.0...0.112.0