a8bd54420b2e3d50e2fd67bfd9dda3c012f76633
markd
  Fri Nov 5 00:36:31 2010 -0700
renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
diff --git src/lib/psl.c src/lib/psl.c
index f52c859..fb623f3 100644
--- src/lib/psl.c
+++ src/lib/psl.c
@@ -1909,34 +1909,34 @@
 char *end = strchr(str, '+');
 if (end)
     {
     *end = 0;
     *ptr = end + 1;
     }
 else 
     *ptr = NULL;
 
 *op = *str++;
 *size = atoi(str);
 
 return TRUE;
 }
 
-struct psl* pslFromCigar(char *qName, int qSize, int qStart, int qEnd,
+struct psl* pslFromGff3Cigar(char *qName, int qSize, int qStart, int qEnd,
                          char *tName, int tSize, int tStart, int tEnd,
                          char* strand, char *cigar)
-/* create a PSL from a cigar formatted alignment */
+/* create a PSL from a GFF3-style cigar formatted alignment */
 {
 // this is currently tested by the gff3ToPsl
 int blocksAlloced = 4;
 struct psl *psl = pslNew(qName, qSize, qStart, qEnd, tName, tSize, tStart, tEnd, strand, blocksAlloced, 0);
 
 char cigarSpec[strlen(cigar+1)];  // copy since parsing is destructive
 strcpy(cigarSpec, cigar);
 char *cigarNext = cigarSpec;
 char op;
 int size;
 int qNext = qStart, qBlkEnd = qEnd;
 if (strand[0] == '-')
     reverseIntRange(&qNext, &qBlkEnd, qSize);
 int tNext = tStart, tBlkEnd = tEnd;
 if (strand[1] == '-')