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/inc/soterm.h src/hg/inc/soterm.h deleted file mode 100644 index e5baaa3..0000000 --- src/hg/inc/soterm.h +++ /dev/null @@ -1,74 +0,0 @@ -/* soterm.h --- Sequence Ontology terms and supporting data structures */ - -#ifndef SOTERM_H -#define SOTERM_H - -enum // the various variant effects - { - regulatory_region_variant=1566, - stop_retained_variant=1567, - splice_acceptor_variant=1574, - splice_donor_variant=1575, - Complex_transcript_variant=1577, - stop_lost=1578, - coding_sequence_variant=1580, - initiator_codon_variant=1582, - missense=1583, - stop_gained=1587, - frameshift_variant=1589, - nc_transcript_variant=1619, - mature_miRNA_variant=1620, - NMD_transcript_variant=1621, - _5_prime_UTR_variant=1623, - _3_prime_UTR_variant=1624, - incomplete_terminal_codon_variant=1626, - intron_variant=1627, - intergenic_variant=1628, - splice_region_variant=1630, - upstream_gene_variant=1631, - downstream_gene_variant=1632, - inframe_deletion=1651, - inframe_insertion=1652, - TF_binding_site_variant=1782, - non_coding_exon_variant=1792, - non_synonymous_variant=1818, - synonymous_variant=1819, - } soTerm; - -struct soCall // a single variant effect call - { - struct soCall *next; - uint soNumber; // Sequence Ontology Number - union - { - struct codingChange // (non)synonymous variant, deletions in CDS - { - char *transcript; - uint exonNumber; - - // the next three should have a length specified too - uint cDnaPosition; - uint cdsPosition; - uint pepPosition; - char *aaChanges; - char *codonChanges; - } codingChange; - struct // intron_variant - { - char *transcript; - uint intronNumber; - } intron; - struct // a generic variant - { - char *soOther0; // Ancillary detail 0 - char *soOther1; // Ancillary detail 1 - char *soOther2; // Ancillary detail 2 - char *soOther3; // Ancillary detail 3 - char *soOther4; // Ancillary detail 4 - char *soOther5; // Ancillary detail 5 - char *soOther6; // Ancillary detail 6 - } generic; - } sub; - }; - -#endif /* SOTERM_H */