<commit_before>package Bio::EnsEMBL::Variation::Utils::Config;

use base qw(Exporter); 

our @EXPORT_OK = qw(@ATTRIB_TYPES @VARIATION_CLASSES @OVERLAP_CONSEQUENCES @FEATURE_TYPES $OVERLAP_CONSEQUENCE_CLASS);

our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence';

our @ATTRIB_TYPES = (
    {
        code => 'SO_accession',
        description => 'Sequence Ontology accession',
    }, 
    {
        code => 'SO_term',
        description => 'Sequence Ontology term',
    },
    {
        code => 'display_term',
        description => 'Ensembl display term',
    },
    {
        code => 'NCBI_term',
        description => 'NCBI term',
    },
    {
        code => 'feature_SO_term',
        description => 'Sequence Ontology term for the associated feature',
    },
    {
        code => 'rank',
        description => 'Relative severity of this variation consequence',
    },
);

our @VARIATION_CLASSES = (
    {
        SO_accession => 'SO:0001483',
        SO_term => 'SNV',
        display_term => 'SNP',
    },
    {
        SO_accession => 'SO:1000002',
        SO_term => 'substitution',
    },
    {
        SO_accession => 'SO:0001019',
        SO_term => 'copy_number_variation',
        display_term => 'CNV',
    },
    {
        SO_accession => 'SO:0000667',
        SO_term => 'insertion',
    },
    {
        SO_accession => 'SO:0000159',
        SO_term => 'deletion',
    },
    {
        SO_accession => 'SO:1000032',
        SO_term => 'indel',
    },
    {
        SO_accession => 'SO:0000705',
        SO_term => 'tandem_repeat',
    },
    {
        SO_accession => 'SO:0001059',
        SO_term => 'sequence_alteration',
    },
);

our @OVERLAP_CONSEQUENCES = (
    {
        SO_accession => 'SO:0001628',
        SO_term => 'intergenic_variant',
        display_term => 'INTERGENIC',
        rank => '100',
        description => 'More than 5 kb either upstream or downstream of a transcript',
        label => 'Intergenic',
    },<commit_msg>add is_default method to OverlapConsequences<commit_after>package Bio::EnsEMBL::Variation::Utils::Config;

use base qw(Exporter); 

our @EXPORT_OK = qw(@ATTRIB_TYPES @VARIATION_CLASSES @OVERLAP_CONSEQUENCES @FEATURE_TYPES $OVERLAP_CONSEQUENCE_CLASS);

our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence';

our @ATTRIB_TYPES = (
    {
        code => 'SO_accession',
        description => 'Sequence Ontology accession',
    }, 
    {
        code => 'SO_term',
        description => 'Sequence Ontology term',
    },
    {
        code => 'display_term',
        description => 'Ensembl display term',
    },
    {
        code => 'NCBI_term',
        description => 'NCBI term',
    },
    {
        code => 'feature_SO_term',
        description => 'Sequence Ontology term for the associated feature',
    },
    {
        code => 'rank',
        description => 'Relative severity of this variation consequence',
    },
);

our @VARIATION_CLASSES = (
    {
        SO_accession => 'SO:0001483',
        SO_term => 'SNV',
        display_term => 'SNP',
    },
    {
        SO_accession => 'SO:1000002',
        SO_term => 'substitution',
    },
    {
        SO_accession => 'SO:0001019',
        SO_term => 'copy_number_variation',
        display_term => 'CNV',
    },
    {
        SO_accession => 'SO:0000667',
        SO_term => 'insertion',
    },
    {
        SO_accession => 'SO:0000159',
        SO_term => 'deletion',
    },
    {
        SO_accession => 'SO:1000032',
        SO_term => 'indel',
    },
    {
        SO_accession => 'SO:0000705',
        SO_term => 'tandem_repeat',
    },
    {
        SO_accession => 'SO:0001059',
        SO_term => 'sequence_alteration',
    },
);

our @OVERLAP_CONSEQUENCES = (
    {
        SO_accession => 'SO:0001628',
        SO_term => 'intergenic_variant',
        display_term => 'INTERGENIC',
        rank => '100',
        description => 'More than 5 kb either upstream or downstream of a transcript',
        label => 'Intergenic',
        is_default => 1,
    },
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