239f153403dc75bf2a57c67ef04dcc7c38e8ecff
angie
  Wed Mar 5 14:03:23 2014 -0800
In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
are any.  I've seen multiple cases of user VCF with indels that
have inflated size due to including right flanking bases; when
trying to determine functional consequences, it's misleading to
have an indel sized larger than it has to be.

diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c
index 80b82c8..c1237df 100644
--- src/hg/hgc/vcfClick.c
+++ src/hg/hgc/vcfClick.c
@@ -348,30 +348,31 @@
     {
     printf("<B>dbVar:</B> ");
     printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
 	   "TARGET=_BLANK>%s</A><BR>\n", rec->name, rec->name);
     }
 printCustomUrl(tdb, rec->name, TRUE);
 static char *formName = "vcfCfgHapCenter";
 printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName());
 cartSaveSession(cart);
 vcfCfgHaplotypeCenter(cart, tdb, tdb->track, FALSE, rec->file, rec->name,
 		      seqName, rec->chromStart, formName);
 printf("</FORM>\n");
 char leftBase = rec->alleles[0][0];
 unsigned int vcfStart = vcfRecordTrimIndelLeftBase(rec);
 boolean showLeftBase = (rec->chromStart == vcfStart+1);
+(void)vcfRecordTrimAllelesRight(rec);
 char *displayAls[rec->alleleCount];
 makeDisplayAlleles(rec, showLeftBase, leftBase, 20, TRUE, FALSE, displayAls);
 printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name);
 printf("<B>Reference allele:</B> %s<BR>\n", displayAls[0]);
 vcfAltAlleleDetails(rec, displayAls);
 vcfQualDetails(rec);
 vcfFilterDetails(rec);
 vcfInfoDetails(rec);
 pgSnpCodingDetail(rec);
 makeDisplayAlleles(rec, showLeftBase, leftBase, 5, FALSE, TRUE, displayAls);
 vcfGenotypesDetails(rec, tdb->track, displayAls);
 }
 
 #ifdef USE_TABIX