38bc9e01ce6e7b22f0533c6624a64a17fd6c7bff
angie
  Fri Sep 27 17:20:54 2013 -0700
Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons.  Now, instead of iterating through
exons and building a new genePred along with a sequence that has
one exon's modification, we project the variant start and end onto
cDNA and CDS coords up front.  Then there is only one modification
to make per allele, and in fact we only care about the actual
modification when there's a CDS change.
A new SO term, exon_loss, has been incorporated into gpFx and
hgVai's/annoGratorGpVar's filtering.
fixes #11771

diff --git src/lib/vcf.c src/lib/vcf.c
index 39178e2..9a5aecf 100644
--- src/lib/vcf.c
+++ src/lib/vcf.c
@@ -1104,30 +1104,30 @@
     allStartSame = FALSE;
 int offset = allStartSame ? 1 : 0;
 if (refAllele[offset] == '\0')
     dyStringAppendC(dy, '-');
 else
     dyStringAppend(dy, refAllele+offset);
 // VCF alternate alleles are comma-separated, make them /-separated:
 altAlleles = words[4];
 if (isNotEmpty(altAlleles) && differentString(altAlleles, "."))
     {
     // Now construct the string:
     while ((p = strchr(altAlleles, ',')) != NULL)
 	{
 	dyStringAppendC(dy, '/');
 	int len = p - altAlleles - offset;
-	if (len == 0)
+	if (len == 0 || startsWith("<DEL>", altAlleles+offset))
 	    dyStringAppendC(dy, '-');
 	else
 	    dyStringAppendN(dy, altAlleles+offset, len);
 	altAlleles = p+1;
 	}
     dyStringAppendC(dy, '/');
     int len = strlen(altAlleles) - offset;
-    if (len == 0)
+    if (len == 0 || startsWith("<DEL>", altAlleles+offset))
 	dyStringAppendC(dy, '-');
     else
 	dyStringAppendN(dy, altAlleles+offset, len);
     }
 return dy->string;
 }