feeb7ee7651d3a85ebc34c4fb32243a841eacdf2
braney
  Mon Apr 16 16:23:04 2012 -0700
on-going work on annoGrator (#6152).  Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
diff --git src/hg/lib/gpFx.c src/hg/lib/gpFx.c
index b30cd05..dc93d33 100644
--- src/hg/lib/gpFx.c
+++ src/hg/lib/gpFx.c
@@ -71,87 +71,104 @@
     struct genePred *pred)
 // check to see if a single variant is in an exon or an intron
 {
 int ii;
 struct gpFx *effectsList = NULL;
 
 for(ii=0; ii < pred->exonCount - 1; ii++)
     {
     // check if in intron
     if (positiveRangeIntersection(pred->exonEnds[ii], 
 	    pred->exonStarts[ii+1],
 	    variant->chromStart, variant->chromEnd))
 	{
 	struct gpFx *effects;
 	AllocVar(effects);
-	effects->gpFxType = gpFxIntron;
-	effects->gpFxNumber = ii;
+	effects->so.soNumber = intron_variant;
+	effects->so.sub.intron.transcript = cloneString(pred->name);
+	effects->so.sub.intron.intronNumber = ii;
 	slAddHead(&effectsList, effects);
 	}
     }
 
 return effectsList;
 }
 
 
 static struct gpFx *gpFxCheckBackground(struct variant *variant, 
     struct genePred *pred)
 // check to see if the variant is up or downstream or in intron of the gene 
 {
 struct gpFx *effectsList = NULL, *effects;
 
 for(; variant ; variant = variant->next)
     {
     // is this variant in an intron
     effectsList = slCat(effectsList, gpFxCheckIntrons(variant, pred));
 
     if (positiveRangeIntersection(pred->txStart - GPRANGE, pred->txStart,
 	    variant->chromStart, variant->chromEnd))
 	{
 	AllocVar(effects);
 	if (*pred->strand == '+')
-	    effects->gpFxType = gpFxUpstream;
+	    ;//effects->gpFxType = gpFxUpstream;
 	else
-	    effects->gpFxType = gpFxDownstream;
+	    ;//ffects->gpFxType = gpFxDownstream;
 	effectsList = slCat(effectsList, effects);
 	}
 
     if (positiveRangeIntersection(pred->txEnd, pred->txEnd + GPRANGE,
 	    variant->chromStart, variant->chromEnd))
 	{
 	AllocVar(effects);
 	if (*pred->strand == '+')
-	    effects->gpFxType = gpFxDownstream;
+	    ;//ffects->gpFxType = gpFxDownstream;
 	else
-	    effects->gpFxType = gpFxUpstream;
+	    ;//ffects->gpFxType = gpFxUpstream;
 	effectsList = slCat(effectsList, effects);
 	}
     }
 
 return effectsList;
 }
 
+static void checkVariantList(struct variant *variant)
+// check to see that we either have one variant (possibly with multiple
+// alleles) or that if we have a list of variants, they only have
+// one allele a piece.
+{
+if (variant->next == NULL)	 // just one variant
+    return;
+
+for(; variant; variant = variant->next)
+    if (variant->numAlleles != 1)
+	errAbort("gpFxPredEffect needs either 1 variant, or only 1 allele in all variants");
+}
+
 struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,
     char **returnTranscript, char **returnCoding)
 // return the predicted effect(s) of a variation list on a genePred
 {
 struct gpFx *effectsList = NULL;
 
+// make sure we can deal with the variants that are coming in
+checkVariantList(variant);
+
 // check to see if SNP is up or downstream in intron 
 effectsList = slCat(effectsList, gpFxCheckBackground(variant, pred));
 
 // check to see if SNP is in the transcript
 effectsList = slCat(effectsList, gpFxCheckExons(variant, pred, 
     returnTranscript, returnCoding));
 
 if (effectsList != NULL)
     return effectsList;
 
 // default is no effect
 struct gpFx *noEffect;
 
 AllocVar(noEffect);
 noEffect->next = NULL;
-noEffect->gpFxType = gpFxNone;
+;//oEffect->gpFxType = gpFxNone;
 
 return noEffect;
 }