Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ANSI_BLACK |
"\u001b[30m" |
public static final String |
ANSI_BLUE |
"\u001b[34m" |
public static final String |
ANSI_CYAN |
"\u001b[36m" |
public static final String |
ANSI_GREEN |
"\u001b[32m" |
public static final String |
ANSI_PURPLE |
"\u001b[35m" |
public static final String |
ANSI_RED |
"\u001b[31m" |
public static final String |
ANSI_RESET |
"\u001b[0m" |
public static final String |
ANSI_WHITE |
"\u001b[37m" |
public static final String |
ANSI_YELLOW |
"\u001b[33m" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_NUM_THREADS |
4 |
protected static final String |
EMPTY_STRING |
"" |
public static final int |
LIMIT |
1000 |
protected static final String |
META |
"meta" |
protected static final String |
REST |
"rest" |
public static final int |
REST_CALL_BATCH_SIZE |
200 |
protected static final String |
WEBSERVICES |
"webservices" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MERGE |
"merge" |
public static final String |
REGION |
"region" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CELLBASE_DATABASES_MONGODB_HOST |
"CELLBASE_DATABASES_MONGODB_HOST" |
public static final String |
CELLBASE_DATABASES_MONGODB_OPTIONS_PREFIX |
"CELLBASE_DATABASES_MONGODB_OPTIONS_" |
public static final String |
CELLBASE_DATABASES_MONGODB_PASSWORD |
"CELLBASE_DATABASES_MONGODB_PASSWORD" |
public static final String |
CELLBASE_DATABASES_MONGODB_USER |
"CELLBASE_DATABASES_MONGODB_USER" |
public static final String |
CELLBASE_PREFIX |
"CELLBASE_" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
GENOTYPE_TAG |
"GT" |
public static final String |
PHASE_SET_TAG |
"PS" |
public static final String |
PHASED_GENOTYPE_SEPARATOR |
"|" |
public static final String |
UNPHASED_GENOTYPE_SEPARATOR |
"/" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
CNV_EXTRA_PADDING |
"cnvExtraPadding" |
protected static final String |
COMPLEMENTARY_START_CODON |
"TAC" |
protected static final String |
DOWN_UP_STREAM_GENE_TAG |
"_gene" |
protected static final String |
IMPRECISE |
"imprecise" |
protected static final String |
MT |
"MT" |
protected static final int |
NO_EXON_OVERLAP |
0 |
protected static final String |
START_CODON |
"ATG" |
protected static final String |
SV_EXTRA_PADDING |
"svExtraPadding" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
BIG_VARIANT_SIZE_THRESHOLD |
50 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AMBIGUOUS_ORF |
"ambiguous_orf" |
public static final String |
ANTISENSE |
"antisense" |
public static final String |
CDS_END_NF |
"cds_end_NF" |
public static final String |
CDS_START_NF |
"cds_start_NF" |
public static final String |
CODING_SEQUENCE_VARIANT |
"coding_sequence_variant" |
public static final String |
COPY_NUMBER_CHANGE |
"copy_number_change" |
public static final String |
DOWNSTREAM_GENE_VARIANT |
"downstream_gene_variant" |
public static final String |
FEATURE_TRUNCATION |
"feature_truncation" |
public static final String |
FEATURE_VARIANT |
"feature_variant" |
public static final String |
FIVE_PRIME_UTR_VARIANT |
"5_prime_UTR_variant" |
public static final String |
FRAMESHIFT_VARIANT |
"frameshift_variant" |
public static final String |
IG_C_GENE |
"IG_C_gene" |
public static final String |
IG_C_PSEUDOGENE |
"IG_C_pseudogene" |
public static final String |
IG_D_GENE |
"IG_D_gene" |
public static final String |
IG_J_GENE |
"IG_J_gene" |
public static final String |
IG_J_PSEUDOGENE |
"IG_J_pseudogene" |
public static final String |
IG_V_GENE |
"IG_V_gene" |
public static final String |
IG_V_PSEUDOGENE |
"IG_V_pseudogene" |
public static final String |
INCOMPLETE_TERMINAL_CODON_VARIANT |
"incomplete_terminal_codon_variant" |
public static final String |
INFRAME_DELETION |
"inframe_deletion" |
public static final String |
INFRAME_INSERTION |
"inframe_insertion" |
public static final String |
INFRAME_VARIANT |
"inframe_variant" |
public static final String |
INITIATOR_CODON_VARIANT |
"initiator_codon_variant" |
public static final String |
INTERGENIC_VARIANT |
"intergenic_variant" |
public static final String |
INTRON_VARIANT |
"intron_variant" |
public static final String |
KNOWN_NCRNA |
"known_ncrna" |
public static final String |
LINCRNA |
"lincRNA" |
public static final String |
LRG_GENE |
"LRG_gene" |
public static final String |
MATURE_MIRNA_VARIANT |
"mature_miRNA_variant" |
public static final String |
MIRNA |
"miRNA" |
public static final String |
MIRNA_PSEUDOGENE |
"miRNA_pseudogene" |
public static final String |
MISC_RNA |
"misc_RNA" |
public static final String |
MISC_RNA_PSEUDOGENE |
"misc_RNA_pseudogene" |
public static final String |
MISSENSE_VARIANT |
"missense_variant" |
public static final String |
MT_RRNA |
"Mt_rRNA" |
public static final String |
MT_TRNA |
"Mt_tRNA" |
public static final String |
NMD_TRANSCRIPT_VARIANT |
"NMD_transcript_variant" |
public static final String |
NON_CODING |
"non_coding" |
public static final String |
NON_CODING_TRANSCRIPT_EXON_VARIANT |
"non_coding_transcript_exon_variant" |
public static final String |
NON_CODING_TRANSCRIPT_VARIANT |
"non_coding_transcript_variant" |
public static final String |
NON_STOP_DECAY |
"non_stop_decay" |
public static final String |
NONSENSE_MEDIATED_DECAY |
"nonsense_mediated_decay" |
public static final String |
POLYMORPHIC_PSEUDOGENE |
"polymorphic_pseudogene" |
public static final String |
PROCESSED_PSEUDOGENE |
"processed_pseudogene" |
public static final String |
PROCESSED_TRANSCRIPT |
"processed_transcript" |
public static final String |
PROTEIN_CODING |
"protein_coding" |
public static final String |
PSEUDOGENE |
"pseudogene" |
public static final String |
REGULATORY_REGION_VARIANT |
"regulatory_region_variant" |
public static final String |
RETAINED_INTRON |
"retained_intron" |
public static final String |
RETROTRANSPOSED |
"retrotransposed" |
public static final String |
RRNA |
"rRNA" |
public static final String |
RRNA_PSEUDOGENE |
"rRNA_pseudogene" |
public static final String |
SCRNA_PSEUDOGENE |
"scRNA_pseudogene" |
public static final String |
SENSE_INTRONIC |
"sense_intronic" |
public static final String |
SENSE_OVERLAPPING |
"sense_overlapping" |
public static final char |
SEPARATOR_CHAR |
58 |
public static final String |
SNORNA |
"snoRNA" |
public static final String |
SNORNA_PSEUDOGENE |
"snoRNA_pseudogene" |
public static final String |
SNRNA |
"snRNA" |
public static final String |
SNRNA_PSEUDOGENE |
"snRNA_pseudogene" |
public static final String |
SPLICE_ACCEPTOR_VARIANT |
"splice_acceptor_variant" |
public static final String |
SPLICE_DONOR_VARIANT |
"splice_donor_variant" |
public static final String |
SPLICE_REGION_VARIANT |
"splice_region_variant" |
public static final String |
START_LOST |
"start_lost" |
public static final String |
START_RETAINED_VARIANT |
"start_retained_variant" |
public static final String |
STOP_GAINED |
"stop_gained" |
public static final String |
STOP_LOST |
"stop_lost" |
public static final String |
STOP_RETAINED_VARIANT |
"stop_retained_variant" |
public static final String |
STRUCTURAL_VARIANT |
"structural_variant" |
public static final String |
SYNONYMOUS_VARIANT |
"synonymous_variant" |
public static final String |
TERMINATOR_CODON_VARIANT |
"terminator_codon_variant" |
public static final String |
TF_BINDING_SITE_VARIANT |
"TF_binding_site_variant" |
public static final String |
THREE_PRIME_UTR_VARIANT |
"3_prime_UTR_variant" |
public static final String |
THREEPRIME_OVERLAPPING_NCRNA |
"3prime_overlapping_ncrna" |
public static final String |
TR_C_GENE |
"TR_C_gene" |
public static final String |
TR_D_GENE |
"TR_D_gene" |
public static final String |
TR_J_GENE |
"TR_J_gene" |
public static final String |
TR_J_PSEUDOGENE |
"TR_J_pseudogene" |
public static final String |
TR_V_GENE |
"TR_V_gene" |
public static final String |
TR_V_PSEUDOGENE |
"TR_V_pseudogene" |
public static final String |
TRANSCRIBED_PROCESSED_PSEUDOGENE |
"transcribed_processed_pseudogene" |
public static final String |
TRANSCRIBED_UNITARY_PSEUDOGENE |
"transcribed_unitary_pseudogene" |
public static final String |
TRANSCRIBED_UNPROCESSED_PSEUDGENE |
"transcribed_unprocessed_pseudogene" |
public static final String |
TRANSCRIPT_ABLATION |
"transcript_ablation" |
public static final String |
TRANSCRIPT_AMPLIFICATION |
"transcript_amplification" |
public static final String |
TRANSLATED_PROCESSED_PSEUDOGENE |
"translated_processed_pseudogene" |
public static final String |
TRANSLATED_UNPROCESSED_PSEUDOGENE |
"translated_unprocessed_pseudogene" |
public static final String |
TRNA_PSEUDOGENE |
"tRNA_pseudogene" |
public static final String |
TWOKB_DOWNSTREAM_VARIANT |
"2KB_downstream_variant" |
public static final String |
TWOKB_UPSTREAM_VARIANT |
"2KB_upstream_variant" |
public static final String |
UNITARY_PSEUDOGENE |
"unitary_pseudogene" |
public static final String |
UNPROCESSED_PSEUDOGENE |
"unprocessed_pseudogene" |
public static final String |
UPSTREAM_GENE_VARIANT |
"upstream_gene_variant" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
IGNORE_PHASE |
"ignorePhase" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
NEIGHBOURING_SEQUENCE_SIZE |
100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CADD_DATA |
"cadd" |
public static final String |
CLINICAL_VARIANTS_ANNOTATED_JSON_FILE |
"clinical_variants.full.json.gz" |
public static final String |
CLINICAL_VARIANTS_DATA |
"clinical_variants" |
public static final String |
CLINICAL_VARIANTS_FOLDER |
"clinicalVariant" |
public static final String |
CLINICAL_VARIANTS_JSON_FILE |
"clinical_variants.json.gz" |
public static final String |
CLINVAR_DATA |
"clinvar" |
public static final String |
CLINVAR_EFO_FILE |
"ClinVar_Traits_EFO_Names.csv" |
public static final String |
CLINVAR_SUMMARY_FILE |
"variant_summary.txt.gz" |
public static final String |
CLINVAR_VARIATION_ALLELE_FILE |
"variation_allele.txt.gz" |
public static final String |
CLINVAR_XML_FILE |
"ClinVarFullRelease_2019-06.xml.gz" |
public static final String |
CONSERVATION_DATA |
"conservation" |
public static final String |
COSMIC_DATA |
"cosmic" |
public static final String |
COSMIC_FILE |
"CosmicMutantExport.tsv.gz" |
public static final String |
DBSNP_FILE |
"All.vcf.gz" |
public static final String |
DGV_FILE |
"dgv.txt" |
public static final String |
DGV_VERSION_FILE |
"dgvVersion.json" |
public static final String |
DISGENET_DATA |
"disgenet" |
public static final String |
DOCM_DATA |
"docm" |
public static final String |
DOCM_FILE |
"docm.json.gz" |
public static final String |
DOCM_NAME |
"DOCM" |
public static final String |
DRUG_DATA |
"drug" |
public static final String |
GENE_DATA |
"gene" |
public static final String |
GENE_DISEASE_ASSOCIATION_DATA |
"gene_disease_association" |
public static final String |
GENOME_DATA |
"genome" |
public static final String |
GENOME_INFO_DATA |
"genome_info" |
public static final String |
GERP_FILE |
"hg19.GERP_scores.tar.gz" |
public static final String |
GERP_SUBDIRECTORY |
"gerp" |
public static final String |
GSD_FILE |
"genomicSuperDups.txt.gz" |
public static final String |
GSD_VERSION_FILE |
"genomicSuperDups.json" |
public static final String |
GWAS_DATA |
"gwas" |
public static final String |
GWAS_FILE |
"gwas_catalog.tsv" |
public static final String |
HPO_DATA |
"hpo" |
public static final String |
IARCTP53_FILE |
"IARC-TP53.zip" |
public static final String |
IARCTP53_GERMLINE_FILE |
"germlineMutationDataIARC TP53 Database, R18.txt" |
public static final String |
IARCTP53_GERMLINE_REFERENCES_FILE |
"germlineMutationReferenceIARC TP53 Database, R18.txt" |
public static final String |
IARCTP53_SOMATIC_FILE |
"somaticMutationDataIARC TP53 Database, R18.txt" |
public static final String |
IARCTP53_SOMATIC_REFERENCES_FILE |
"somaticMutationReferenceIARC TP53 Database, R18.txt" |
public static final String |
MOTIF_FEATURES_FILE |
"motiffeatures.gff.gz" |
public static final String |
PPI_DATA |
"ppi" |
public static final String |
PROTEIN_DATA |
"protein" |
public static final String |
PROTEIN_FUNCTIONAL_PREDICTION_DATA |
"protein_functional_prediction" |
public static final String |
REGULATION_DATA |
"regulation" |
public static final String |
REGULATORY_FEATURES_FILE |
"Regulatory_Build.regulatory_features.gff.gz" |
public static final String |
REPEATS_DATA |
"repeats" |
public static final String |
REPEATS_FOLDER |
"repeats" |
public static final String |
REPEATS_JSON |
"repeats" |
public static final String |
STRUCTURAL_VARIANTS_DATA |
"svs" |
public static final String |
STRUCTURAL_VARIANTS_FOLDER |
"structuralVariants" |
public static final String |
STRUCTURAL_VARIANTS_JSON |
"structuralVariants" |
public static final String |
TRF_FILE |
"simpleRepeat.txt.gz" |
public static final String |
TRF_VERSION_FILE |
"simpleRepeat.json" |
public static final String |
VARIATION_DATA |
"variation" |
public static final String |
VARIATION_FUNCTIONAL_SCORE_DATA |
"variation_functional_score" |
public static final String |
WM_FILE |
"windowMasker.txt.gz" |
public static final String |
WM_VERSION_FILE |
"windowMasker.json" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CONSERVATION_CHUNK_SIZE |
2000 |
public static final int |
GENE_CHUNK_SIZE |
5000 |
public static final int |
GENOME_SEQUENCE_CHUNK_SIZE |
2000 |
public static final int |
REGULATORY_REGION_CHUNK_SIZE |
2000 |
public static final int |
REPEATS_CHUNK_SIZE |
2000 |
public static final int |
VARIATION_CHUNK_SIZE |
2000 |
public static final int |
VARIATION_FUNCTIONAL_SCORE_CHUNK_SIZE |
1000 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
HAPLOTYPE_FIELD_NAME |
"haplotype" |
protected static final char |
HAPLOTYPE_STRING_SEPARATOR |
44 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
EFO_ID |
"EFO id" |
public static final String |
EFO_NAME |
"EFO name" |
public static final String |
EFO_URL |
"EFO URL" |
public static final String |
GRCH37_ASSEMBLY |
"37" |
public static final String |
GRCH38_ASSEMBLY |
"38" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PREPROCESSED_VARIATION_FEATURE_FILENAME |
"variation_feature.sorted.txt" |
public static final String |
VARIATION_FEATURE_FILENAME |
"variation_feature.txt" |
public static final int |
VARIATION_ID_COLUMN_INDEX_IN_VARIATION_FEATURE_FILE |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PREPROCESSED_VARIATION_FILENAME |
"variation.sorted.txt" |
public static final int |
RS_COLUMN_INDEX |
2 |
public static final String |
VARIATION_FILENAME |
"variation.txt" |
public static final int |
VARIATION_ID_COLUMN_INDEX |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
PREPROCESSED_VARIATION_FILENAME |
"variation.sorted.txt" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PREPROCESSED_VARIATION_SYNONYM_FILENAME |
"variation_synonym.sorted.txt" |
public static final String |
VARIATION_SYNONYM_FILENAME |
"variation_synonym.txt" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PREPROCESSED_TRANSCRIPT_VARIATION_FILENAME |
"transcript_variation.includingVariationId.txt" |
public static final String |
TRANSCRIPT_VARIATION_FILENAME |
"transcript_variation.txt" |
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