Option to store the alignments in a non-temporary file

[eclarke]

The alignments could be useful for downstream debugging. Could there be an option to save the bwa/bowtie SAM file?

[anatolydryga]

i find it useful too. The only one requirement is use BAM not SAM
it saves order of magnitude of disk space

[anatolydryga]

@kylebittinger maybe add --debug option to save all of the intermediate files