Is your feature request related to a problem? Please specify.

As i understand it, samtools fastq currently allows outputs reads "as-is" from the BAM. If they were hard-clipped then they are already existing in clipped form and output as such, but if they are soft-clipped, and i want the clipped reads out, I can not get them (?)

Describe the solution you would like.

Would like a new option for samtools fastq to obvserve the soft clipping in the CIGAR and output the shorter clipped reads.