STAR/HiSAT2 output coordinate sorted BAM

[lindaxiang]

@akahles Can we sort STAR/HiSAT2 output BAMs by coordinate? Otherwise the index file can not be built.

[akahles]

We usually do this as a downstream process after alignment. The STAR sorting (at least in the past) was not very efficient and using samtools view knew that the output was compatible with downstream tools.

[lindaxiang]

This has been addressed.