Create sam format for collapse_isoforms_by_sam.py

[rodrisenovilla]

Hi! Thank you for your package!

I am trying to use collapse_isoforms_by_sam.py as part of another pipeline (https://github.com/Gaius-Augustus/BRAKER/blob/master/docs/long_reads/long_read_protocol.md).

The main problem is that your test_data/hq_isoforms.fastq.sorted.sam is quite different from mine following the same sorting. I am using a new assemblied genome, so I guess that sorting might have to be different? Or maybe related to the headers of the genome?

The .sam file works well when visualizing the alignment on IGV, but I haven't passed any other quality test.

I would be happy to send you any other detail or file! Thank you very much, Rodrigo Senovilla