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/gpFx.h src/hg/inc/gpFx.h index 0f55a90..bc69c42 100644 --- src/hg/inc/gpFx.h +++ src/hg/inc/gpFx.h @@ -1,27 +1,29 @@ #ifndef GPFX_H #define GPFX_H #include "variant.h" -#include "soterm.h" +#include "soTerm.h" // a single gpFx variant effect call struct gpFx { struct gpFx *next; - -struct soCall so; + char *allele; // Allele sequence used to determine functional effect + struct soCall so; // Sequence Ontology ID of effect and plus associated data }; struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred, struct dnaSeq *transcriptSequence); // return the predicted effect(s) of a variation list on a genePred // number of bases up or downstream that we flag -#define GPRANGE 500 +#define GPRANGE 5000 #define gpFxIsCodingChange(gpfx) (gpfx->so.soNumber == inframe_deletion || \ + gpfx->so.soNumber == inframe_insertion || \ gpfx->so.soNumber == frameshift_variant || \ gpfx->so.soNumber == synonymous_variant || \ - gpfx->so.soNumber == non_synonymous_variant) + gpfx->so.soNumber == missense_variant || \ + gpfx->so.soNumber == stop_gained) #endif /* GPFX_H */