src/hg/hgTracks/cds.c 1.96

1.96 2009/05/24 09:10:38 mikep
Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence

Index: src/hg/hgTracks/cds.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/cds.c,v
retrieving revision 1.95
retrieving revision 1.96
diff -b -B -U 4 -r1.95 -r1.96
--- src/hg/hgTracks/cds.c	20 May 2009 20:50:51 -0000	1.95
+++ src/hg/hgTracks/cds.c	24 May 2009 09:10:38 -0000	1.96
@@ -832,8 +832,14 @@
     mrnaSeq = newDnaSeq(cloneString(name), strlen(name), cloneString(name));
     if (lf->orientation == -1)
 	reverseComplement(mrnaSeq->dna, mrnaSeq->size);
     }
+else if (sameString("seq1Seq2", seqSource))
+    {
+    mrnaSeq = lf->extra;
+    if (lf->orientation == -1)
+	reverseComplement(mrnaSeq->dna, mrnaSeq->size);
+    }
 else
     mrnaSeq = hGenBankGetMrna(database, name, NULL);
 
 if (mrnaSeq != NULL)