whale_merge.py sequence naming

[dhoconno]

Hi there,

I'm not sure if others have had this issue, but the naming convention of fused reads in whale_merge.py can be problematic for htslib/samtools.

Samtools throws the error:

[E::sam_parse1] query name too long
[W::sam_read1] Parse error at line 281431
[main_samview] truncated file.

This also affects other tools that rely on samtools.

This seems to occur when multiple reads are fused together and are named with XX|YY|ZZ... and the length of the query exceeds 251 characters as described here: pysam-developers/pysam#447

A possible solution would be to slice the FASTQ name to 250 characters or fewer.

Thanks,

dave

[dhoconno]

I think an easy workaround is to just slice on the first N characters of the header in whale_merge.py:

readheadelements[0] = readhead[0:240]

Cheers,

dave