src/lib/pslTransMap.c 1.8

Index: src/lib/pslTransMap.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/pslTransMap.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/lib/pslTransMap.c	11 Mar 2008 21:19:31 -0000	1.7
+++ src/lib/pslTransMap.c	2 Nov 2009 05:17:38 -0000	1.8
@@ -100,8 +100,22 @@
 psl->tStarts[newIBlk] = blk->tStart;
 psl->blockSizes[newIBlk] = blk->qEnd - blk->qStart;
 /* lie about match counts. */
 psl->match += psl->blockSizes[newIBlk];
+/* count gaps */
+if (newIBlk > 0)
+    {
+    if (psl->qStarts[newIBlk] > pslQEnd(psl, newIBlk-1))
+        {
+        psl->qNumInsert++;
+        psl->qBaseInsert += psl->qStarts[newIBlk] - pslQEnd(psl, newIBlk-1);
+        }
+    if (psl->tStarts[newIBlk] > pslTEnd(psl, newIBlk-1))
+        {
+        psl->tNumInsert++;
+        psl->tBaseInsert += psl->tStarts[newIBlk] - pslTEnd(psl, newIBlk-1);
+        }
+    }
 psl->blockCount++;
 }
 
 static void setPslBounds(struct psl* mappedPsl)