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chadlaing / Panseq

Pan-genomic sequence analysis
http://lfz.corefacility.ca/panseq
GNU General Public License v3.0
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show-coords called incorrectly in NucmerRun.pm #1

Closed ctberthiaume closed 10 years ago

ctberthiaume commented 10 years ago

The show-coords command of MUMmer is called incorrectly (at least with respect to the verison of MUMmer I'm running) in NucmerRun.pm. The order of options and delta file input argument were reversed. Modified line 219 in NucmerRun.pm should be

my $coordsLine = $self->mummerDirectory . 'show-coords -l -q -T ' . $deltaFile . ' > ' . $self->coordsFile;

This bug at a minimum caused some tests in t/output.t to fail. I tested with Panseq commit ab3704d0c, MUMmer version 3.23, MUSCLE version 3.8.31, and BLAST version 2.2.28+. After the above modification all tests passed.