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

use base qw(Exporter); 

our @EXPORT_OK = qw(
    @ATTRIB_TYPES 
    %ATTRIBS
    @ATTRIB_SETS
    @VARIATION_CLASSES 
    @OVERLAP_CONSEQUENCES 
    @FEATURE_TYPES 
    $OVERLAP_CONSEQUENCE_CLASS
    $MAX_ATTRIB_CODE_LENGTH
);

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

our $MAX_ATTRIB_CODE_LENGTH = 20;

our @short_names = qw(1kg_hct 1kg_hct_ceu 1kg_hct_yri 1kg_hce 1kg_hce_ceu 1kg_hce_chb
                      1kg_hce_chd 1kg_hce_jpt 1kg_hce_lwk 1kg_hce_tsi 1kg_hce_yri 1kg_lc
	                      1kg_lc_ceu 1kg_lc_chb_jpt 1kg_lc_yri 1kg_hq hapmap
                      1kg 1kg_afr 1kg_amr 1kg_asn 1kg_eur 1kg_com 1kg_afr_com 1kg_amr_com 1kg_asn_com 1kg_eur_com
                      ind_venter ind_watson ind_gill ind_ak1 ind_irish ind_angrist
                      ind_gates_jr ind_gates_sr ind_kriek ind_quake ind_saqqaq ind_saqqaq_hc ind_sjk ind_yh
                      fail_all fail_nonref fail_ambig fail_gt_fq fail_incons_map fail_mult_map
                      fail_no_alleles fail_no_gt fail_no_map fail_no_seq fail_non_nt fail_mult_alleles fail_dbsnp_suspect
                      ph_hgmd_pub ph_nhgri ph_omim ph_variants ph_uniprot
                      ph_cosmic ph_ega  hapmap_ceu hapmap_hcb hapmap_jpt hapmap_yri
                      Affy_500K Affy_SNP6 Cardio-Metabo_Chip HumanOmni1-Quad Illumina_1M-duo Illumina_660Q
                      Human610_Quad HumanHap550 HumanHap650Y HumanOmni2.5 PorcineSNP60
                      esp_6500 clin_assoc 
                     );

our @dbsnp_clinical_significance_types = qw(
    unknown
    untested
    non-pathogenic
    probable-non-pathogenic
    probable-pathogenic
    pathogenic
    drug-response
    histocompatibility
    other
);

our @dgva_clinical_significance_types = (
    'Not tested',
    'Benign',
    'Pathogenic',
    'Uncertain Significance',
    'Uncertain Significance: likely benign',
    'Uncertain Significance: likely pathogenic'
);
<commit_msg>added short names for new genotyping chips<commit_after>package Bio::EnsEMBL::Variation::Utils::Config;

use base qw(Exporter); 

our @EXPORT_OK = qw(
    @ATTRIB_TYPES 
    %ATTRIBS
    @ATTRIB_SETS
    @VARIATION_CLASSES 
    @OVERLAP_CONSEQUENCES 
    @FEATURE_TYPES 
    $OVERLAP_CONSEQUENCE_CLASS
    $MAX_ATTRIB_CODE_LENGTH
);

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

our $MAX_ATTRIB_CODE_LENGTH = 20;

our @short_names = qw(1kg_hct 1kg_hct_ceu 1kg_hct_yri 1kg_hce 1kg_hce_ceu 1kg_hce_chb
                      1kg_hce_chd 1kg_hce_jpt 1kg_hce_lwk 1kg_hce_tsi 1kg_hce_yri 1kg_lc
	                      1kg_lc_ceu 1kg_lc_chb_jpt 1kg_lc_yri 1kg_hq hapmap
                      1kg 1kg_afr 1kg_amr 1kg_asn 1kg_eur 1kg_com 1kg_afr_com 1kg_amr_com 1kg_asn_com 1kg_eur_com
                      ind_venter ind_watson ind_gill ind_ak1 ind_irish ind_angrist
                      ind_gates_jr ind_gates_sr ind_kriek ind_quake ind_saqqaq ind_saqqaq_hc ind_sjk ind_yh
                      fail_all fail_nonref fail_ambig fail_gt_fq fail_incons_map fail_mult_map
                      fail_no_alleles fail_no_gt fail_no_map fail_no_seq fail_non_nt fail_mult_alleles fail_dbsnp_suspect
                      ph_hgmd_pub ph_nhgri ph_omim ph_variants ph_uniprot
                      ph_cosmic ph_ega  hapmap_ceu hapmap_hcb hapmap_jpt hapmap_yri
                      Affy_500K Affy_SNP6 Cardio-Metabo_Chip HumanOmni1-Quad Illumina_1M-duo Illumina_660Q
                      Human610_Quad HumanHap550 HumanHap650Y HumanOmni2.5 PorcineSNP60
                      esp_6500 clin_assoc 
                      Chicken600K EquineSNP50 BovineHD BovineLD BovineSNP50   
                     );

our @dbsnp_clinical_significance_types = qw(
    unknown
    untested
    non-pathogenic
    probable-non-pathogenic
    probable-pathogenic
    pathogenic
    drug-response
    histocompatibility
    other
);

our @dgva_clinical_significance_types = (
    'Not tested',
    'Benign',
    'Pathogenic',
    'Uncertain Significance',
    'Uncertain Significance: likely benign',
    'Uncertain Significance: likely pathogenic'
);

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