04c67a0e7bcb65c217598e5e44084bf4c5c0674d angie Tue Mar 5 12:16:10 2013 -0800 Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output. diff --git src/hg/lib/soTerm.c src/hg/lib/soTerm.c new file mode 100644 index 0000000..73bf437 --- /dev/null +++ src/hg/lib/soTerm.c @@ -0,0 +1,43 @@ +/* soTerm - Sequence Ontology terms that we use for compatibility with Ensembl & others. */ + +#include "common.h" +#include "soTerm.h" + +char *soTermToString(enum soTerm termNumber) +/* Translate termNumber to its string equivalent. Do not modify or free result. */ +{ +switch (termNumber) + { + case regulatory_region_variant : return "regulatory_region_variant"; break; + case stop_retained_variant : return "stop_retained_variant"; break; + case splice_acceptor_variant : return "splice_acceptor_variant"; break; + case splice_donor_variant : return "splice_donor_variant"; break; + case complex_transcript_variant : return "complex_transcript_variant"; break; + case stop_lost : return "stop_lost"; break; + case coding_sequence_variant : return "coding_sequence_variant"; break; + case initiator_codon_variant : return "initiator_codon_variant"; break; + case missense_variant : return "missense_variant"; break; + case stop_gained : return "stop_gained"; break; + case frameshift_variant : return "frameshift_variant"; break; + case nc_transcript_variant : return "nc_transcript_variant"; break; + case mature_miRNA_variant : return "mature_miRNA_variant"; break; + case NMD_transcript_variant : return "NMD_transcript_variant"; break; + case _5_prime_UTR_variant : return "5_prime_UTR_variant"; break; + case _3_prime_UTR_variant : return "3_prime_UTR_variant"; break; + case incomplete_terminal_codon_variant : return "incomplete_terminal_codon_variant"; break; + case intron_variant : return "intron_variant"; break; + case intergenic_variant : return "intergenic_variant"; break; + case splice_region_variant : return "splice_region_variant"; break; + case upstream_gene_variant : return "upstream_gene_variant"; break; + case downstream_gene_variant : return "downstream_gene_variant"; break; + case TF_binding_site_variant : return "TF_binding_site_variant"; break; + case non_coding_exon_variant : return "non_coding_exon_variant"; break; + case protein_altering_variant : return "protein_altering_variant"; break; + case synonymous_variant : return "synonymous_variant"; break; + case inframe_deletion : return "inframe_deletion"; break; + case inframe_insertion : return "inframe_insertion"; break; + default: + errAbort("soTermToString: don't recognize term %u", termNumber); + } +return "ERROR"; // never get here +}