-dev-head-1'.

Sprout from master 2008-02-14 08:57:57 UTC Glenn Proctor <gp1@sanger.ac.uk> 'Fix job naming.'
Cherrypick from master 2009-04-15 12:17:55 UTC Kerstin Howe <kj2@sanger.ac.uk> 'added FOS ends for zebrafish':
    misc-scripts/analysis_description/analysis.descriptions
    misc-scripts/analysis_description/apply_rules.pl
    misc-scripts/analysis_description/chech_web_data_column.pl
    misc-scripts/analysis_description/load_analysis_descriptions.pl
    misc-scripts/canonical_transcripts/set_canonical_transcripts.pl
    misc-scripts/db-space.pl
    misc-scripts/ebi_search_dump/ebi_search_dump.pl
    misc-scripts/id_mapping/synteny_rescore.pl
    misc-scripts/id_mapping/utils/compare_scores.pl
    misc-scripts/misc_feature/misc_set.descriptions
    misc-scripts/misc_feature/update_misc_set_descripitons.pl
    misc-scripts/translation_attribs.pl
    misc-scripts/translation_attribs_wrapper.pl
    misc-scripts/update_mapping_set.pl
    misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
    misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
    misc-scripts/xref_mapping/XrefMapper/Interpro.pm
    misc-scripts/xref_mapping/XrefMapper/LoadMapper.pm
    misc-scripts/xref_mapping/XrefMapper/ProcessMappings.pm
    misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm
    misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
    misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
    misc-scripts/xref_mapping/XrefMapper/TestMappings.pm
    misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_willistoni.pm
    misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm
    misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
    misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm
    misc-scripts/xref_mapping/XrefParser/HGNC_curated_transcriptParser.pm
    misc-scripts/xref_mapping/XrefParser/HPAParser.pm
    misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm
    misc-scripts/xref_mapping/XrefParser/MGI_CCDS_Parser.pm
    misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
    misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm
    misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm
    misc-scripts/xref_mapping/XrefParser/Vega_TranParser.pm
    misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
    misc-scripts/xref_mapping/xref_tracker.pl
    modules/Bio/EnsEMBL/Collection.pm
    modules/Bio/EnsEMBL/Collection/Exon.pm
    modules/Bio/EnsEMBL/Collection/Gene.pm
    modules/Bio/EnsEMBL/Collection/RepeatFeature.pm
    modules/Bio/EnsEMBL/Collection/Transcript.pm
    modules/Bio/EnsEMBL/DBSQL/GOTermAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
    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/AedesAegypti.pm
    modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
    modules/Bio/EnsEMBL/OntologyTerm.pm
    modules/t/test-genome-DBs/homo_sapiens/core/mapping_set.sql
    modules/t/test-genome-DBs/homo_sapiens/core/mapping_set.txt
    modules/t/test-genome-DBs/homo_sapiens/core/seq_region_mapping.sql
    modules/t/test-genome-DBs/homo_sapiens/core/seq_region_mapping.txt
    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
    sql/patch_50_51_a.sql
    sql/patch_50_51_b.sql
    sql/patch_50_51_c.sql
    sql/patch_50_51_d.sql
    sql/patch_50_51_e.sql
    sql/patch_50_51_f.sql
    sql/patch_50_51_g.sql
    sql/patch_50_51_h.sql
    sql/patch_50_51_i.sql
    sql/patch_51_52_a.sql
    sql/patch_51_52_b.sql
    sql/patch_51_52_c.sql
    sql/patch_51_52_d.sql
    sql/patch_52_53_a.sql
    sql/patch_52_53_b.sql
    sql/patch_52_53_c.sql
    sql/patch_52_53_d.sql
    sql/patch_53_54_a.sql
    sql/patch_53_54_b.sql
    sql/patch_53_54_c.sql
Delete:
    misc-scripts/protein_match/process_pmach.pl
    modules/Bio/EnsEMBL/Collection/DnaAlignFeature.pm
    modules/Bio/EnsEMBL/Collection/ProteinAlignFeature.pm
    modules/Bio/EnsEMBL/DBSQL/Clone.pm