Member AssemblyMapper::BlastzAligner::filter_overlaps ()

. This filtering algorithm didn't work well. Please run the separate script fix_overlaps.pl.

Member Bio::EnsEMBL::DBSQL::TranscriptAdaptor::store ()

(optional) Int $analysis_id The analysis_id to use when storing this gene. This is for backward compatibility only and used to fall back to the gene analysis_id if no analysis object is attached to the transcript (which you should do for new code). Arg [4] : prevent coordinate recalculation if you are persisting transcripts with this gene Example :

Member Bio::EnsEMBL::Feature::add_sub_SeqFeature ()

- only for genebuild backward compatibility. Avoid using it if possible

Member Bio::EnsEMBL::Feature::flush_sub_SeqFeature ()

- Only for genebuild backwards compatibility. Avoid using it if possible

Member Bio::EnsEMBL::Feature::sub_SeqFeature ()

- For genebuild backwards compatibility. Avoid using it if possible

Member Bio::EnsEMBL::Utils::Exception::deprecate ()

Example :

method was called. Deprecated warnings only appear once for each location the method was called from. No message is displayed if the level of verbosity is lower than the level of the warning. Returntype : none Exceptions : warning every time Caller :

methods

. Also prints the line number and file from which the

Member parse_deleted_files ()

Read list of deleted gene and transcript stable IDs from file(s). Note that this method of determining which objects were deleted is now

(because it was error-prone when dealing with both whole gene and individual transcript deletions). Return type : none Exceptions : thrown on missing files Caller : main() Status : At Risk : under development