Improve output stats

[colindaven]

@LisaHollstein

[colindaven]

Hi @LisaHollstein I've added a dev branch and tried to only output mapped reads to the SAM file, instead of all reads as previously done. Please test.

[LisaHollstein]

Hi!
I think it works. When I tested it the bt.test.sam file was empty despite the lines with headers, which makes sense since there are 0 lines with 3 Ns after masking accordins to the stats.
(The stats say there is 1 line in the file without a header. Is @HD a header or does it mean something else?)

[colindaven]

Sounds good. You can check the Sam file with less for a header called @hd and exclude with the grep -v cmd in the shell script.