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Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
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Bio::FeatureIO::gff::_handle_feature bug in method #127

Open cjfields opened 9 years ago

cjfields commented 9 years ago

Author Name: Emmanuel Quevillon (Emmanuel Quevillon) Original Redmine Issue: 3314, https://redmine.open-bio.org/issues/3314 Original Date: 2011-11-15 Original Assignee: Chris Fields

There is a coding error that causes ‘_handle_feature’ to crash line 592.

Description: After sorted gff3 file using gff3_gff3_preprocessor.pl to sort GFF3 file, and using gmod_bulk_load_gff3.pl script, the following error is thrown:

Can’t call method “end” on an undefined value at /usr/local/share/perl/5.10.1/Bio/FeatureIO/gff.pm line 592.

This can be fixed by surrounding the following expression with parenthesis :

$start < $region->start() || $end > $region->end() as below

($start < $region->start() || $end > $region->end())

This code modification fixes the problem. I attached a diff file to show the modification as a gff example file to test it.

Regards

Emmanuel

cjfields commented 9 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2011-11-15T14:04:58Z

Note, this code has moved to a separate repository. I’ll take a look at it.

cjfields commented 9 years ago

Original Redmine Comment Author Name: Emmanuel Quevillon Original Date: 2011-11-15T14:06:23Z

Chris Fields wrote:

Note, this code has moved to a separate repository. I’ll take a look at it.

Where should I have to look then? Thanks Chris

cjfields commented 9 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2011-12-11T03:43:24Z

Emmanuel Quevillon wrote:

Chris Fields wrote:

Note, this code has moved to a separate repository. I’ll take a look at it.

Where should I have to look then? Thanks Chris

It’s on github