Feature request: write bam rather than sam

[wdecoster]

Hi,

Although I haven't been able to run it to completion (see other issues), I noticed your tool writes a sam file, but it would be hugely beneficial (for storage) that this would be directly written or converted to bam. Perhaps you can pipe the output to samtools view -o myalignment.bam. Sam files would be really problematic for bigger amount of MinION data or a couple of samples of PromethION data. We never write sam.

Cheers,
Wouter