Windows linebreaks lead to crash

[philippbayer]

Hello,

When a FASTQ quality line ends with \r\n instead of \n SNAP crashes with the error-message:

Syntax error in FASTQ file at offset 71. Quality string is of the wrong length.

This Python line generates a read that leads to the above error-message:

open('broken_read.fq','w').write(''.join(['@SEQ_ID\n', 'GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT\n', '+\n', "!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65\r\n"]))

Not that hard to circumvent but a bit hard to catch in the first place...

[mateiz]

Good catch! Somewhat ironic since quite a few of the developers are on Windows, but we'll fix it.

[rnpandya]

Fixed with commit d127a4ab