GitLab

added condition to check there is a funcgen database for the variation database before checking for regulatory features

ensembl-50'.

Sprout from branch-ensembl-49 2008-07-04 10:31:09 UTC Stephen Keenan <keenan@ebi.ac.uk> '*** empty log message ***'
Cherrypick from master 2008-07-10 10:14:21 UTC Daniel Rios <dr2@sanger.ac.uk> 'new tables to handle user upload data':
    misc-scripts/id_mapping/synteny_rescore.pl
    misc-scripts/id_mapping/utils/compare_scores.pl
    modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
    modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
    modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblGeneGeneric.pm
    modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
    modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
    sql/patch_49_50_a.sql
    sql/patch_49_50_b.sql
    sql/patch_49_50_c.sql
    sql/patch_49_50_d.sql
    sql/patch_49_50_e.sql

ensembl-49'.

Sprout from master 2008-03-06 11:56:44 UTC Eugene Kulesha <ek@ebi.ac.uk> 'take care of the situations when source type presented by a variable rather than a array'
Delete:
    misc-scripts/protein_match/process_pmach.pl
    modules/Bio/EnsEMBL/DBSQL/Clone.pm

a string that can be 0 (zero).

Similarly use "if (exists( some hash compartment ))" for the same reason.

A couple of changes from "@{ function_returning_array_ref() }($index)"
to "function_returning_array_ref()->[$index]";

General cleanup in comments and code.

Passes the unit tests.

Proper new() for most classes:
  * $class = ref($proto) || $proto;
  * Setting attributes the same way.

Format the getter and setters the same way, especially in
Mapper/Coordinate.pm, getting rid of unneccesary shifts.

sprintf() formatting including '%1$s'.

Minor formatting.

and later into Ensembl release 50.