src/jkOwnLib/gfPcrLib.c 1.12

Index: src/jkOwnLib/gfPcrLib.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/jkOwnLib/gfPcrLib.c,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 4 -r1.11 -r1.12
--- src/jkOwnLib/gfPcrLib.c	23 Sep 2009 18:42:27 -0000	1.11
+++ src/jkOwnLib/gfPcrLib.c	7 Dec 2009 18:24:00 -0000	1.12
@@ -264,11 +264,20 @@
 fprintf(f, "0\t%d\t", size);	/* qStart, qEnd */
 fprintf(f, "%s\t%d\t", out->seqName, out->seqSize);
 fprintf(f, "%d\t%d\t", out->fPos, out->rPos);
 fprintf(f, "2\t");
-fprintf(f, "%d,%d,\t", fPrimerSize, rPrimerSize);
-fprintf(f, "%d,%d,\t", 0,size - rPrimerSize);
-fprintf(f, "%d,%d,\n", out->fPos, out->rPos - rPrimerSize);
+if (out->strand == '+')
+    {
+    fprintf(f, "%d,%d,\t", fPrimerSize, rPrimerSize);
+    fprintf(f, "%d,%d,\t", 0,size - rPrimerSize);
+    fprintf(f, "%d,%d,\n", out->fPos, out->rPos - rPrimerSize);
+    }
+else
+    {
+    fprintf(f, "%d,%d,\t", rPrimerSize, fPrimerSize);
+    fprintf(f, "%d,%d,\t", 0,size - fPrimerSize);
+    fprintf(f, "%d,%d,\n", out->fPos, out->rPos - fPrimerSize);
+    }
 }
 
 typedef void (*outFunction)(struct gfPcrOutput *out, FILE *f, char *url) ;