#1 tarchive2amos seq/qual length discrepancy

open
nobody
None
5
2006-11-28
2006-11-28
Dave Messina
No

Hi,

This is a patch for tarchive2amos from AMOS 2.0.0. I am on OS X 10.4.8 with Perl 5.8.6.

When trying to convert a sequence in FASTA format and its corresponding quality file, I encounter:

% ../amos-2.0.0/bin/tarchive2amos -o test test.seq
Parsing test.seq and test.qual
Died at /Users/davemessina/Desktop/amos-2.0.0/lib/AMOS/AmosFoundation.pm line 272, <QUAL> line 44.
Exit 2

This is due to a limitation in the regex on line 529 of tarchive2amos.

The attached tarball includes the test.seq and test.qual which can be used to reproduce the bug, and a patch to fix tarchive2amos.

Hope this helps,
Dave

Discussion

  • Dave Messina
    Dave Messina
    2006-11-28

    tarchive2amos qual file bug patch