src/jkOwnLib/genoFind.c 1.26

Index: src/jkOwnLib/genoFind.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/jkOwnLib/genoFind.c,v
retrieving revision 1.25
retrieving revision 1.26
diff -b -B -U 4 -r1.25 -r1.26
--- src/jkOwnLib/genoFind.c	20 Mar 2008 17:39:43 -0000	1.25
+++ src/jkOwnLib/genoFind.c	8 Oct 2009 18:09:38 -0000	1.26
@@ -2190,4 +2190,52 @@
 reverseComplement(rPrimer, rPrimerSize);
 return clumpList;
 }
 
+int gfDefaultRepMatch(int tileSize, int stepSize, boolean protTiles)
+/* Figure out appropriate step repMatch value. */
+{
+int repMatch = 1024;
+if (protTiles)
+    {
+    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
+        internalErr();
+    }
+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;
+    else
+        internalErr();
+    }
+repMatch *= tileSize;
+repMatch /= stepSize;
+return repMatch;
+}