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Bio::SearchIO : bug when parsing TBlastX and method matches of Bio::SearchIO::Hit #128

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Frederic Sapet (Frederic Sapet) Original Redmine Issue: 3319, https://redmine.open-bio.org/issues/3319 Original Date: 2012-01-25 Original Assignee: Bioperl Guts

Hello

When I try to parse a TBLASTX file, I have got an error message :

——————- EXCEPTION: Bio::Root::Exception ——————- MSG: Undefined sub-sequence (575,575). Valid range = 99 - 575 STACK: Error::throw STACK: Bio::Root::Root::throw /home/fsapet/BioPerlLive/lib/perl5/Bio/Root/Root.pm:472 STACK: Bio::Search::HSP::HSPI::matches /home/fsapet/BioPerlLive/lib/perl5/Bio/Search/HSP/HSPI.pm:716 STACK: Bio::Search::SearchUtils::_adjust_contigs /home/fsapet/BioPerlLive/lib/perl5/Bio/Search/SearchUtils.pm:515 STACK: Bio::Search::SearchUtils::tile_hsps /home/fsapet/BioPerlLive/lib/perl5/Bio/Search/SearchUtils.pm:201 STACK: Bio::Search::Hit::GenericHit::matches /home/fsapet/BioPerlLive/lib/perl5/Bio/Search/Hit/GenericHit.pm:896

BioPerl.version

49.46.48.48.54.57.48.50

perl.version

This is perl, v5.10.0 built for x86_64-linux-thread-multi

Fred