src/utils/faSplit/faSplit.c 1.37

Index: src/utils/faSplit/faSplit.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/faSplit/faSplit.c,v
retrieving revision 1.36
retrieving revision 1.37
diff -b -B -U 4 -r1.36 -r1.37
--- src/utils/faSplit/faSplit.c	22 May 2010 18:50:33 -0000	1.36
+++ src/utils/faSplit/faSplit.c	23 May 2010 03:13:53 -0000	1.37
@@ -463,8 +463,12 @@
 	char numOut[128];
 	int thisSize = seq.size - pos;
 	if (thisSize > (pieceSize + extra)) 
 	    thisSize = pieceSize + extra;
+
+	if ((thisSize <= extra) && (pos > 0))
+	    break;  /* nobody wants duplicate smaller than extra overhang */
+
 	if (bitCountRange(bits, pos, thisSize) <= maxN)
 	    {
 	    if (!oneFile)
 	        {