#132 convert-fasta-to-v2.pl

Assembly_pipeline
closed
Brian Walenz
Utility (7)
5
2012-01-06
2011-12-19
Simon
No

If anybody is interested I have added a few lines to this script to die and report if any vector clear coordinate is longer than its corresponding read. I have seen this condition a few times in the trace archive data and convert-fasta-to-v2.pl happily builds the FRG file without complaining.

This is the diff to the cvs version from 16 Dec. 2011:

228,232d227
< my @vecClr = split(',', $clv{$seqid});
< my $readLength = length($seq);
< if( $vecClr[1] > $readLength ) {
< die "Read $seqid has vector clear range ($vecClr[1]) longer than read length ($readLength).\n";
< }

Discussion

  • Brian Walenz
    Brian Walenz
    2012-01-06

    • assigned_to: nobody --> brianwalenz
    • status: open --> closed