Erroneous 'region_not_covered' in v4.7.0 #2054
Description
When I use a custom IG library and run the following command using v4.7.0, I get erroneous 'region_not_covered' outputs for the majority of sequences in the 'nMutationsVRegion' when I have exported only functional clones:
mixcr analyze generic-amplicon -t 20 \ --floating-left-alignment-boundary \ --floating-right-alignment-boundary C \ --rna \ --species Bos_taurus \ --library Bostaurus-IGH.json.gz \ --assemble-clonotypes-by VDJRegion \ /home/tpursell/BulkIgFastqs/B18-FLU247-Leader-IGH_S7_L001_R1_001.fastq.gz \ /home/tpursell/BulkIgFastqs/B18-FLU247-Leader-IGH_S7_L001_R2_001.fastq.gz \ /home/tpursell/BulkIgFastqs/mixcr.outs.bota.20260107/bota.B18.FLU247.FSleader
Attached is the alignment report for one of the samples; it shows that 93% of sequences cover the VDJregion so I should not have the error exporting the mutations for the VRegion.