src/blat/blat.c 1.113

1.113 2009/02/10 21:58:55 kent
Makin blat work with U's instead of T's if q=rna is set.

Index: src/blat/blat.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/blat/blat.c,v
retrieving revision 1.112
retrieving revision 1.113
diff -b -B -U 4 -r1.112 -r1.113
--- src/blat/blat.c	25 Nov 2007 17:17:55 -0000	1.112
+++ src/blat/blat.c	10 Feb 2009 21:58:55 -0000	1.113
@@ -306,8 +306,10 @@
 Bits *qMaskBits = maskQuerySeq(seq, isProt, maskQuery, lcMask);
 struct dnaSeq trimmedSeq;
 ZeroVar(&trimmedSeq);
 trimSeq(seq, &trimmedSeq);
+if (qType == gftRna || qType == gftRnaX)
+   memSwapChar(trimmedSeq.dna, trimmedSeq.size, 'u', 't');
 searchOne(&trimmedSeq, gf, outFile, isProt, maskHash, qMaskBits);
 *retTotalSize += seq->size;
 *retCount += 1;
 bitFree(&qMaskBits);