77ce65f9c4bbe25ed64d5892c9835baa0704581a
kent
  Tue Oct 25 17:57:23 2011 -0700
Finishing implementing minSize option.
diff --git src/isPcr/isPcr/isPcr.c src/isPcr/isPcr/isPcr.c
index d0e2f5b..fbf5515 100644
--- src/isPcr/isPcr/isPcr.c
+++ src/isPcr/isPcr/isPcr.c
@@ -145,32 +145,34 @@
 	minRepDivergence, showStatus);
 gf = gfIndexSeq(dbSeqList, 2, 2, tileSize, repMatch, ooc, 
     FALSE, 0, mask != NULL, stepSize);
 
 lf = lineFileOpen(queryFile, TRUE);
 while (lineFileRow(lf, row))
     {
     struct gfPcrInput gpi;
     gfPcrInputStaticLoad(row, &gpi);
     verbose(2, "PCR on %s %s %s\n", gpi.name, gpi.fPrimer, gpi.rPrimer);
     if (strlen(gpi.fPrimer) < 11 || strlen(gpi.rPrimer) < 11)
             errAbort("Primer too short (<10): %s %s %s", 
                                 gpi.name, gpi.fPrimer, gpi.rPrimer);
     if (flipReverse)
         reverseComplement(gpi.rPrimer, strlen(gpi.rPrimer));
-    pcrStrand(gf, gpi.name, gpi.fPrimer, gpi.rPrimer, 0, maxSize, '+', out, f);
-    pcrStrand(gf, gpi.name, gpi.fPrimer, gpi.rPrimer, 0, maxSize, '-', out, f);
+    pcrStrand(gf, gpi.name, gpi.fPrimer, gpi.rPrimer, minSize, maxSize, 
+    	'+', out, f);
+    pcrStrand(gf, gpi.name, gpi.fPrimer, gpi.rPrimer, minSize, maxSize, 
+    	'-', out, f);
     }
 lineFileClose(&lf);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 ooc = optionVal("ooc", ooc);
 tileSize = optionInt("tileSize", tileSize);
 stepSize = optionInt("stepSize", stepSize);
 maxSize = optionInt("maxSize", maxSize);