LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

SYNOPSIS

DESCRIPTION

METHODS

find_non_overlaps

   Args       : arrayref of B::E::Transcripts
   Example    : find_non_overlaps($all_transcripts)
   Description: identifies any non-overlapping transcripts
   Returntype : array refs of stable IDs
   Exceptions : none

check_remarks_and_update_names

   Arg[1]     : B::E::Gene (with potentially duplicated transcript names)
   Arg[2]     : counter 1 (no. of patched genes)
   Arg[3]     : counter 2 (no. of patched transcripts)
   Example    : $support->update_names($gene,\$c1,\$c2)
   Description: - checks remarks and patches transcripts with identical names according to
                CDS and length
   Returntype : true | false (depending on whether patched or not), counter1, counter2

check_names_and_overlap

   Arg[1]     : arayref of arrayrefs of duplicated names
   Arg[2]     : B::E::Gene (with potentially duplicated transcript names)
   Arg[3]     : FH (to log new duplicates)
   Example    : $support->check_names_and_overlap($transcripts,$gene,$fh)
   Description: checks pairs of transcripts identified as having duplicate Vega names:
                - to see if they have identical names in loutre (shouldn't have)
                - distinguish between overlapping and non overlapping transcripts
   Returntype : none

get_havana_fragmented_loci_comments

   Args       : none
   Example    : my $results = $support->get_havana_fragmented_loci_comments
   Description: parses the HEREDOC containing Havana comments in this module
   Returntype : hashref