Constant Field Values

Contents

• org.monarchinitiative.*

org.monarchinitiative.*

org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey

Modifier and Type	Constant Field	Value
public static final int	ALT_FIELD_NUMBER	4
public static final int	CHR_FIELD_NUMBER	1
public static final int	POSITION_FIELD_NUMBER	2
public static final int	REF_FIELD_NUMBER	3

org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties

Modifier and Type	Constant Field	Value
public static final int	CLINVAR_FIELD_NUMBER	3
public static final int	FREQUENCIES_FIELD_NUMBER	4
public static final int	PATHOGENICITYSCORES_FIELD_NUMBER	5
public static final int	PROPERTIES_FIELD_NUMBER	2
public static final int	RS_ID_FIELD_NUMBER	1

org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar

Modifier and Type	Constant Field	Value
public static final int	ALLELEID_FIELD_NUMBER	1
public static final int	CLIN_SIG_COUNTS_FIELD_NUMBER	12
public static final int	GENE_ID_FIELD_NUMBER	8
public static final int	GENE_SYMBOL_FIELD_NUMBER	7
public static final int	HGVS_CDNA_FIELD_NUMBER	10
public static final int	HGVS_PROTEIN_FIELD_NUMBER	11
public static final int	INCLUDEDALLELES_FIELD_NUMBER	5
public static final int	PRIMARYINTERPRETATION_FIELD_NUMBER	2
public static final int	REVIEWSTATUS_FIELD_NUMBER	4
public static final int	SECONDARYINTERPRETATIONS_FIELD_NUMBER	3
public static final int	VARIANT_EFFECT_FIELD_NUMBER	9
public static final int	VARIATIONID_FIELD_NUMBER	6

org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig

Modifier and Type	Constant Field	Value
public static final int	AFFECTS_VALUE	9
public static final int	ASSOCIATION_VALUE	10
public static final int	BENIGN_OR_LIKELY_BENIGN_VALUE	2
public static final int	BENIGN_VALUE	1
public static final int	CONFLICTING_PATHOGENICITY_INTERPRETATIONS_VALUE	8
public static final int	DRUG_RESPONSE_VALUE	11
public static final int	LIKELY_BENIGN_VALUE	3
public static final int	LIKELY_PATHOGENIC_VALUE	5
public static final int	NOT_PROVIDED_VALUE	0
public static final int	OTHER_VALUE	12
public static final int	PATHOGENIC_OR_LIKELY_PATHOGENIC_VALUE	6
public static final int	PATHOGENIC_VALUE	7
public static final int	PROTECTIVE_VALUE	13
public static final int	RISK_FACTOR_VALUE	14
public static final int	UNCERTAIN_SIGNIFICANCE_VALUE	4

org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ReviewStatus

Modifier and Type	Constant Field	Value
public static final int	CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS_VALUE	4
public static final int	CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS_VALUE	5
public static final int	CRITERIA_PROVIDED_SINGLE_SUBMITTER_VALUE	3
public static final int	NO_ASSERTION_CRITERIA_PROVIDED_VALUE	1
public static final int	NO_ASSERTION_PROVIDED_VALUE	0
public static final int	NO_INTERPRETATION_FOR_THE_SINGLE_VARIANT_VALUE	2
public static final int	PRACTICE_GUIDELINE_VALUE	7
public static final int	REVIEWED_BY_EXPERT_PANEL_VALUE	6

org.monarchinitiative.exomiser.core.proto.AlleleProto.Frequency

Modifier and Type	Constant Field	Value
public static final int	AC_FIELD_NUMBER	3
public static final int	AN_FIELD_NUMBER	4
public static final int	FREQUENCY_FIELD_NUMBER	2
public static final int	FREQUENCYSOURCE_FIELD_NUMBER	1
public static final int	HOM_FIELD_NUMBER	5

org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource

Modifier and Type	Constant Field	Value
public static final int	ALFA_AFA_VALUE	57
public static final int	ALFA_AFO_VALUE	56
public static final int	ALFA_AFR_VALUE	58
public static final int	ALFA_ASN_VALUE	64
public static final int	ALFA_EAS_VALUE	63
public static final int	ALFA_EUR_VALUE	59
public static final int	ALFA_LAC_VALUE	60
public static final int	ALFA_LEN_VALUE	61
public static final int	ALFA_OAS_VALUE	65
public static final int	ALFA_OTR_VALUE	66
public static final int	ALFA_SAS_VALUE	62
public static final int	ALFA_TOT_VALUE	67
public static final int	ESP_AA_VALUE	5
public static final int	ESP_ALL_VALUE	6
public static final int	ESP_EA_VALUE	4
public static final int	GNOMAD_E_AFR_VALUE	16
public static final int	GNOMAD_E_AMR_VALUE	17
public static final int	GNOMAD_E_ASJ_VALUE	18
public static final int	GNOMAD_E_EAS_VALUE	19
public static final int	GNOMAD_E_FIN_VALUE	20
public static final int	GNOMAD_E_MID_VALUE	24
public static final int	GNOMAD_E_NFE_VALUE	21
public static final int	GNOMAD_E_OTH_VALUE	22
public static final int	GNOMAD_E_SAS_VALUE	23
public static final int	GNOMAD_G_AFR_VALUE	36
public static final int	GNOMAD_G_AMI_VALUE	44
public static final int	GNOMAD_G_AMR_VALUE	37
public static final int	GNOMAD_G_ASJ_VALUE	38
public static final int	GNOMAD_G_EAS_VALUE	39
public static final int	GNOMAD_G_FIN_VALUE	40
public static final int	GNOMAD_G_MID_VALUE	45
public static final int	GNOMAD_G_NFE_VALUE	41
public static final int	GNOMAD_G_OTH_VALUE	42
public static final int	GNOMAD_G_SAS_VALUE	43
public static final int	KG_VALUE	1
public static final int	LOCAL_VALUE	7
public static final int	TOPMED_VALUE	2
public static final int	UK10K_VALUE	3
public static final int	UNSPECIFIED_FREQUENCY_SOURCE_VALUE	0

org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicityScore

Modifier and Type	Constant Field	Value
public static final int	PATHOGENICITYSOURCE_FIELD_NUMBER	1
public static final int	SCORE_FIELD_NUMBER	2

org.monarchinitiative.exomiser.core.proto.AlleleProto.PathogenicitySource

Modifier and Type	Constant Field	Value
public static final int	ALPHA_MISSENSE_VALUE	11
public static final int	CADD_VALUE	6
public static final int	CLINVAR_VALUE	15
public static final int	DBVAR_VALUE	14
public static final int	EVE_VALUE	12
public static final int	MUTATION_TASTER_VALUE	4
public static final int	MVP_VALUE	9
public static final int	POLYPHEN_VALUE	3
public static final int	REMM_VALUE	7
public static final int	REVEL_VALUE	8
public static final int	SIFT_VALUE	5
public static final int	SPLICE_AI_VALUE	10
public static final int	TEST_VALUE	2
public static final int	UNKNOWN_PATH_SOURCE_VALUE	0
public static final int	VARIANT_EFFECT_VALUE	1

org.monarchinitiative.exomiser.core.proto.AlleleProto.VariantEffect

Modifier and Type	Constant Field	Value
public static final int	CHROMOSOME_NUMBER_VARIATION_VALUE	1
public static final int	CODING_SEQUENCE_VARIANT_VALUE	58
public static final int	CODING_TRANSCRIPT_INTRON_VARIANT_VALUE	34
public static final int	CODING_TRANSCRIPT_VARIANT_VALUE	63
public static final int	COMPLEX_SUBSTITUTION_VALUE	15
public static final int	CONSERVED_INTERGENIC_VARIANT_VALUE	56
public static final int	CONSERVED_INTRON_VARIANT_VALUE	54
public static final int	COPY_NUMBER_CHANGE_VALUE	13
public static final int	DIRECT_TANDEM_DUPLICATION_VALUE	42
public static final int	DISRUPTIVE_INFRAME_DELETION_VALUE	26
public static final int	DISRUPTIVE_INFRAME_INSERTION_VALUE	24
public static final int	DOWNSTREAM_GENE_VARIANT_VALUE	46
public static final int	EXON_LOSS_VARIANT_VALUE	3
public static final int	EXON_VARIANT_VALUE	60
public static final int	FEATURE_TRUNCATION_VALUE	11
public static final int	FIVE_PRIME_UTR_EXON_VARIANT_VALUE	36
public static final int	FIVE_PRIME_UTR_INTRON_VARIANT_VALUE	38
public static final int	FIVE_PRIME_UTR_PREMATURE_START_CODON_GAIN_VARIANT_VALUE	35
public static final int	FIVE_PRIME_UTR_TRUNCATION_VALUE	27
public static final int	FRAMESHIFT_ELONGATION_VALUE	7
public static final int	FRAMESHIFT_TRUNCATION_VALUE	8
public static final int	FRAMESHIFT_VARIANT_VALUE	9
public static final int	INFRAME_DELETION_VALUE	25
public static final int	INFRAME_INSERTION_VALUE	23
public static final int	INITIATOR_CODON_VARIANT_VALUE	32
public static final int	INSERTION_VALUE	5
public static final int	INTERGENIC_VARIANT_VALUE	47
public static final int	INTERNAL_FEATURE_ELONGATION_VALUE	10
public static final int	INTRAGENIC_VARIANT_VALUE	55
public static final int	INTRON_VARIANT_VALUE	59
public static final int	INVERSION_VALUE	4
public static final int	MIRNA_VALUE	62
public static final int	MISSENSE_VARIANT_VALUE	22
public static final int	MNV_VALUE	14
public static final int	MOBILE_ELEMENT_DELETION_VALUE	43
public static final int	MOBILE_ELEMENT_INSERTION_VALUE	44
public static final int	NON_CODING_TRANSCRIPT_EXON_VARIANT_VALUE	40
public static final int	NON_CODING_TRANSCRIPT_INTRON_VARIANT_VALUE	41
public static final int	NON_CODING_TRANSCRIPT_VARIANT_VALUE	64
public static final int	RARE_AMINO_ACID_VARIANT_VALUE	21
public static final int	REGULATORY_REGION_ABLATION_VALUE	52
public static final int	REGULATORY_REGION_AMPLIFICATION_VALUE	53
public static final int	REGULATORY_REGION_VARIANT_VALUE	51
public static final int	SEQUENCE_VARIANT_VALUE	0
public static final int	SPLICE_ACCEPTOR_VARIANT_VALUE	19
public static final int	SPLICE_DONOR_VARIANT_VALUE	20
public static final int	SPLICE_REGION_VARIANT_VALUE	30
public static final int	SPLICING_VARIANT_VALUE	61
public static final int	START_LOST_VALUE	18
public static final int	STOP_GAINED_VALUE	16
public static final int	STOP_LOST_VALUE	17
public static final int	STOP_RETAINED_VARIANT_VALUE	31
public static final int	STRUCTURAL_VARIANT_VALUE	57
public static final int	SYNONYMOUS_VARIANT_VALUE	33
public static final int	TF_BINDING_SITE_VARIANT_VALUE	50
public static final int	TFBS_ABLATION_VALUE	48
public static final int	TFBS_AMPLIFICATION_VALUE	49
public static final int	THREE_PRIME_UTR_EXON_VARIANT_VALUE	37
public static final int	THREE_PRIME_UTR_INTRON_VARIANT_VALUE	39
public static final int	THREE_PRIME_UTR_TRUNCATION_VALUE	28
public static final int	TRANSCRIPT_ABLATION_VALUE	2
public static final int	TRANSCRIPT_AMPLIFICATION_VALUE	12
public static final int	TRANSLOCATION_VALUE	6
public static final int	UPSTREAM_GENE_VARIANT_VALUE	45

org.monarchinitiative.lirical.cli.Main

Modifier and Type	Constant Field	Value
public static final String	FOOTER	"\nSee the full documentation at https://thejacksonlaboratory.github.io/LIRICAL/stable"
public static final String	VERSION	"lirical v2.1.1-SNAPSHOT"
public static final int	WIDTH	120

org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand

Modifier and Type	Constant Field	Value
protected static final String	UNKNOWN_VERSION_PLACEHOLDER	"UNKNOWN VERSION"

org.monarchinitiative.lirical.cli.cmd.OutputCommand

Modifier and Type	Constant Field	Value
protected static final String	UNKNOWN_VERSION_PLACEHOLDER	"UNKNOWN VERSION"

org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand

Modifier and Type	Constant Field	Value
protected static final String	UNKNOWN_VERSION_PLACEHOLDER	"UNKNOWN VERSION"

org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand

Modifier and Type	Constant Field	Value
protected static final String	UNKNOWN_VERSION_PLACEHOLDER	"UNKNOWN VERSION"

org.monarchinitiative.lirical.cli.cmd.YamlCommand

Modifier and Type	Constant Field	Value
protected static final String	UNKNOWN_VERSION_PLACEHOLDER	"UNKNOWN VERSION"

org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand

Modifier and Type	Constant Field	Value
protected static final String	UNKNOWN_VERSION_PLACEHOLDER	"UNKNOWN VERSION"

org.monarchinitiative.lirical.core.likelihoodratio.PhenotypeLikelihoodRatio

Modifier and Type	Constant Field	Value
public static final float	DEFAULT_TERM_FREQUENCY	1.0f

org.monarchinitiative.lirical.core.service.VariantMetadataService

Modifier and Type	Constant Field	Value
public static final float	DEFAULT_FREQUENCY	0.0010000000474974513f

org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore

Modifier and Type	Constant Field	Value
public static final float	MTASTER_THRESHOLD	0.9399999976158142f

org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore

Modifier and Type	Constant Field	Value
public static final int	EQUAL	0
public static final int	LESS_PATHOGENIC	1
public static final int	MORE_PATHOGENIC	-1

org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PolyPhenScore

Modifier and Type	Constant Field	Value
public static final float	POLYPHEN_PROB_DAMAGING_THRESHOLD	0.9559999704360962f
public static final float	POLYPHEN_THRESHOLD	0.44600000977516174f

org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.SiftScore

Modifier and Type	Constant Field	Value
public static final float	SIFT_THRESHOLD	0.05999999865889549f

org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore

Modifier and Type	Constant Field	Value
public static final float	DEFAULT_HIGH_SCORE	1.0f
public static final float	DEFAULT_MISSENSE_SCORE	0.6000000238418579f
public static final float	FRAMESHIFT_SCORE	1.0f
public static final float	INVERSION_SCORE	0.6000000238418579f
public static final float	NON_PATHOGENIC_SCORE	0.0f
public static final float	NONFRAMESHIFT_INDEL_SCORE	0.8500000238418579f
public static final float	NONSENSE_SCORE	1.0f
public static final float	SPLICE_DONOR_ACCEPTOR_SCORE	1.0f
public static final float	SPLICE_REGION_SCORE	0.800000011920929f
public static final float	STARTLOSS_SCORE	1.0f
public static final float	STOPLOSS_SCORE	1.0f
public static final float	SYNONYMOUS_SCORE	0.10000000149011612f

org.monarchinitiative.lirical.io.output.DifferentialDiagnosis

Modifier and Type	Constant Field	Value
protected static final String	EMPTY_STRING	""
protected static final String	NOT_AVAILABLE	"n/a"

org.monarchinitiative.lirical.io.output.LiricalTemplate

Modifier and Type	Constant Field	Value
protected static final String	EMPTY_STRING	""

org.monarchinitiative.lirical.io.output.TsvDifferential

Modifier and Type	Constant Field	Value
protected static final String	EMPTY_STRING	""
protected static final String	NOT_AVAILABLE	"n/a"

org.monarchinitiative.lirical.io.output.svg.Lirical2Svg

Modifier and Type	Constant Field	Value
protected static final String	BLACK	"#000000"
protected static final String	BLUE	"#4dbbd5"
protected static final int	BOX_HEIGHT	15
protected static final int	BOX_OFFSET	10
protected static final String	BRIGHT_GREEN	"#00a087"
protected static final String	BROWN	"#7e6148"
protected static final String	DARKBLUE	"#3c5488"
protected static final String	GREEN	"#00A087"
protected static final int	MIN_VERTICAL_OFFSET	10
protected static final String	ORANGE	"#ff9900"
protected static final String	RED	"#e64b35"
protected static final String	VIOLET	"#8491b4"