Provide greater detail when BAM sort order is incorrect.

[cerebis]

Hi Matthew,

thanks for your reply. Indeed I can confirm that my bam file does not contain the expected header:

$> samtools view -H L79851_Track-123454.aligned.sorted.bam| grep '^@HD'
@HD     VN:1.6  SO:unknown

The bam files were generated as follows:

samtools sort -n [aligned.bam] -o [aligned.sorted.bam]

However, the logs for that particular step are missing so I will regenerate just to be sure.

Originally posted by @agilly in https://github.com/cerebis/qc3C/issues/58#issuecomment-1034540210