src/blat/blat.c 1.114

Index: src/blat/blat.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/blat/blat.c,v
retrieving revision 1.113
retrieving revision 1.114
diff -b -B -U 4 -r1.113 -r1.114
--- src/blat/blat.c	10 Feb 2009 21:58:55 -0000	1.113
+++ src/blat/blat.c	8 Oct 2009 18:09:38 -0000	1.114
@@ -627,9 +627,9 @@
 
 int main(int argc, char *argv[])
 /* Process command line into global variables and call blat. */
 {
-boolean dIsProtLike, qIsProtLike;
+boolean tIsProtLike, qIsProtLike;
 
 #ifdef DEBUG
 {
 char *cmd = "blat hCrea.geno hCrea.mrna foo.psl -t=dnax -q=rnax";
@@ -658,15 +658,15 @@
 switch (tType)
     {
     case gftProt:
     case gftDnaX:
-        dIsProtLike = TRUE;
+        tIsProtLike = TRUE;
 	break;
     case gftDna:
-        dIsProtLike = FALSE;
+        tIsProtLike = FALSE;
 	break;
     default:
-	dIsProtLike = FALSE;
+	tIsProtLike = FALSE;
         errAbort("Illegal value for 't' parameter");
 	break;
     }
 if (optionExists("q"))
@@ -686,13 +686,13 @@
     default:
         qIsProtLike = FALSE;
 	break;
     }
-if ((dIsProtLike ^ qIsProtLike) != 0)
+if ((tIsProtLike ^ qIsProtLike) != 0)
     errAbort("d and q must both be either protein or dna");
 
 /* Set default tile size for protein-based comparisons. */
-if (dIsProtLike)
+if (tIsProtLike)
     {
     tileSize = 5;
     minMatch = 1;
     oneOff = FALSE;
@@ -709,9 +709,9 @@
 minScore = optionInt("minScore", minScore);
 maxGap = optionInt("maxGap", maxGap);
 minRepDivergence = optionFloat("minRepDivergence", minRepDivergence);
 minIdentity = optionFloat("minIdentity", minIdentity);
-gfCheckTileSize(tileSize, dIsProtLike);
+gfCheckTileSize(tileSize, tIsProtLike);
 if (minMatch < 0)
     errAbort("minMatch must be at least 1");
 if (maxGap > 100)
     errAbort("maxGap must be less than 100");
@@ -722,46 +722,9 @@
  * to reasonable value that depends on tile size. */
 if (optionExists("repMatch"))
     repMatch = optionInt("repMatch", repMatch);
 else
-    {
-    if (dIsProtLike)
-	{
-	if (tileSize == 3)
-	    repMatch = 600000;
-	else if (tileSize == 4)
-	    repMatch = 30000;
-	else if (tileSize == 5)
-	    repMatch = 1500;
-	else if (tileSize == 6)
-	    repMatch = 75;
-	else if (tileSize <= 7)
-	    repMatch = 10;
-	}
-    else
-	{
-	if (tileSize == 15)
-	    repMatch = 16;
-	else if (tileSize == 14)
-	    repMatch = 32;
-	else if (tileSize == 13)
-	    repMatch = 128;
-	else if (tileSize == 12)
-	    repMatch = 256;
-	else if (tileSize == 11)
-	    repMatch = 4*256;
-	else if (tileSize == 10)
-	    repMatch = 16*256;
-	else if (tileSize == 9)
-	    repMatch = 64*256;
-	else if (tileSize == 8)
-	    repMatch = 256*256;
-	else if (tileSize == 7)
-	    repMatch = 1024*256;
-	else if (tileSize == 6)
-	    repMatch = 4*1024*256;
-	}
-    }
+    repMatch = gfDefaultRepMatch(tileSize, stepSize, tIsProtLike);
 
 /* Gather last few command line options. */
 noHead = optionExists("noHead");
 ooc = optionVal("ooc", NULL);