rsem-tbam2gbam soft-clipping (and other) errors

[joegeorgeson]

Hi team RSEM,

I noticed that your rsem-tbam2gbam function doesn't handle soft-clipped reads or multi-mapped reads well, and that there are a handful of other strange cases where a read maps fine in the transcriptome-mapping but gets mapped incorrectly at the genome level. It would be really great (for me, and I hope others too) if you could build this function to be a bit more 'robust' by adding some flags to handle clipping as well as handle multi-mapping cases.

Thanks for a great tool!