bda72d5101dc3eb814a30d6cafbe4bfab6a4d553
angie
  Fri Jun 14 11:16:43 2013 -0700
Fix corner case (deletion falls across exon boundary; normally we wantto trim the part of the allele that falls outside, but for the deletion
the allele is "").

diff --git src/hg/lib/variant.c src/hg/lib/variant.c
index 72c470d..5014abd 100644
--- src/hg/lib/variant.c
+++ src/hg/lib/variant.c
@@ -1,124 +1,119 @@
 /* variant.c -- routines to convert other variant formats to a generic
  *              variant structure */
 
 #include "common.h"
 #include "variant.h"
 
 struct allele  *alleleClip(struct allele *allele, int sx, int ex, struct lm *lm)
 /* Return new allele pointing to new variant, both clipped to region defined by [sx,ex). */
 {
 struct variant *oldVariant = allele->variant;
 int start = oldVariant->chromStart;
 int end = oldVariant->chromEnd;
-int oldVariantWidth = end - start;
 int delFront = 0;
 int delRear = 0;
 
 if (start < sx)
     {
-    if (oldVariantWidth != allele->length)	 /* FIXME */
-	errAbort("cannot clip alleles that are a different length than variant region");
-    delFront = sx - start;
+    delFront = min(sx - start, allele->length);
     start = sx;
     }
 
 if (end > ex)
     {
-    if (oldVariantWidth != allele->length)	 /* FIXME */
-	errAbort("cannot clip alleles that are a different length than variant region");
-    delRear = end - ex;
+    delRear = min(end - ex, allele->length - delFront);
     end = ex;
     }
 
 struct variant *newVariant;
 lmAllocVar(lm, newVariant);
 newVariant->chrom = lmCloneString(lm, oldVariant->chrom);
 newVariant->chromStart = start;
 newVariant->chromEnd = end;
 newVariant->numAlleles = 1;
 
 struct allele *newAllele;
 lmAllocVar(lm, newAllele);
 newVariant->alleles = newAllele;
 newAllele->variant = newVariant;
 newAllele->length = allele->length - delRear - delFront;
 assert(newAllele->length >= 0);
 newAllele->sequence = lmCloneString(lm, &allele->sequence[delFront]);
 newAllele->sequence[newAllele->length] = 0;   // cut off delRear part
 
 return newAllele;
 }
 
 static boolean isDash(char *string)
 /* Return TRUE if the only char in string is '-'
  * (possibly repeated like the darn pgVenter alleles). */
 {
 char *p;
 for (p = string;  p != NULL && *p != '\0';  p++)
     if (*p != '-')
 	return FALSE;
 return TRUE;
 }
 
 struct variant *variantNew(char *chrom, unsigned start, unsigned end, unsigned numAlleles,
 			   char *slashSepAlleles, struct lm *lm)
 /* Create a variant from basic information that is easy to extract from most other variant
  * formats: coords, allele count, and string of slash-separated alleles. */
 {
 struct variant *variant;
 
 // We have a new variant!
 lmAllocVar(lm, variant);
 variant->chrom = lmCloneString(lm, chrom);
 variant->chromStart = start;
 variant->chromEnd = end;
 variant->numAlleles = numAlleles;
 
 // get the alleles.
 char *nextAlleleString = lmCloneString(lm, slashSepAlleles);
 int alleleNumber = 0;
 for( ; alleleNumber < numAlleles; alleleNumber++)
     {
     if (nextAlleleString == NULL)
 	errAbort("number of alleles in pgSnp doesn't match number in name");
     
     char *thisAlleleString = nextAlleleString;
 
     // advance pointer to next variant string
     // probably there's some kent routine to do this behind the curtain
     nextAlleleString = strchr(thisAlleleString, '/');
     if (nextAlleleString)	 // null out '/' and move to next char
 	{
 	*nextAlleleString = 0;
 	nextAlleleString++;
 	}
 
     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);
     }
 
 slReverse(&variant->alleles);
 
 return variant;
 }
 
 struct variant *variantFromPgSnp(struct pgSnp *pgSnp, struct lm *lm)
 /* convert pgSnp record to variant record */
 {
 return variantNew(pgSnp->chrom, pgSnp->chromStart, pgSnp->chromEnd, pgSnp->alleleCount,
 		  pgSnp->name, lm);
 }