fffb0ceba7685b27ca84238e4bd3093c9fd669d3
angie
  Mon Nov 18 15:53:49 2013 -0800
Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
Made improvements to the display of symbolic alleles from dbSNP.
Fixed strand bug in parseDbSnpAltAlleles.  Thanks Jonathan!
refs #11460 (hgVai: paste/upload variant input options)

diff --git src/hg/lib/variant.c src/hg/lib/variant.c
index f49537a..623a6f8 100644
--- src/hg/lib/variant.c
+++ src/hg/lib/variant.c
@@ -91,31 +91,30 @@
     boolean isRefAllele = (sameWord(thisAlleleString, refAllele) ||
 			   (isEmpty(refAllele) && sameString(thisAlleleString, "-")));
     int alleleStringLength = strlen(thisAlleleString);
     if (isDash(thisAlleleString))
 	{
 	alleleStringLength = 0;
 	thisAlleleString[0] = '\0';
 	}
 
     // we have a new allele!
     struct allele *allele;
     AllocVar(allele);
     slAddHead(&variant->alleles, allele);
     allele->variant = variant;
     allele->length = alleleStringLength; 
-    toLowerN(thisAlleleString, alleleStringLength);
     allele->sequence = lmCloneString(lm, thisAlleleString);
     allele->isReference = isRefAllele;
     }
 
 slReverse(&variant->alleles);
 
 return variant;
 }
 
 struct variant *variantFromPgSnp(struct pgSnp *pgSnp, char *refAllele, struct lm *lm)
 /* convert pgSnp record to variant record */
 {
 return variantNew(pgSnp->chrom, pgSnp->chromStart, pgSnp->chromEnd, pgSnp->alleleCount,
 		  pgSnp->name, refAllele, lm);
 }