Output Mate Cigar and Mate Quality tags for each read

[abolia]

Hi, This is not a bug but I think it could be a good future improvement. It would be great to have tags related to mate quality and cigar (MQ and MC) for each read in the bam as well. Latest deduping tools such as PicardUMIAwareMarkDuplicate requires them, so if not for all, is there is a command line option to add these if users want, that would be awesome. From our latest analysis on a large targeted capture data, results showed that Whisper takes half the time of BWA-MEM (thats great !!) but the bams are not compatible with downstream processes as it lacks these missing mate tags and one has to add these through other some other tool which ends up increasing the total run-time of the whisper workflow.

Thanks, Ashini