29d2ec27d938e51aa1748eddf5c608c499410b29
max
  Sun Sep 16 23:22:33 2012 -0700
bugfix: -noMask had no effect when -bed was set
diff --git src/utils/twoBitToFa/twoBitToFa.c src/utils/twoBitToFa/twoBitToFa.c
index fef0c61..95028a7 100644
--- src/utils/twoBitToFa/twoBitToFa.c
+++ src/utils/twoBitToFa/twoBitToFa.c
@@ -126,30 +126,32 @@
 /* Get sequences defined by beds.  Exclude introns. */
 {
 struct bed *bed, *bedList = bedLoadAll(bedFileName);
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
     struct dnaSeq *seq = twoBitAndBedToSeq(tbf, bed);
     char* seqName = NULL;
     if (clBedPos) 
         {
         char buf[1024];
         safef(buf, 1024, "%s:%d-%d", bed->chrom, bed->chromStart, bed->chromEnd);
         seqName = buf;
         }
     else
         seqName = seq->name;
+    if (noMask)
+        toUpperN(seq->dna, seq->size);
     faWriteNext(outFile, seqName, seq->dna, seq->size);
     dnaSeqFree(&seq);
     }
 }
 
 void twoBitToFa(char *inName, char *outName)
 /* twoBitToFa - Convert all or part of twoBit file to fasta. */
 {
 struct twoBitFile *tbf;
 FILE *outFile = mustOpen(outName, "w");
 struct twoBitSpec *tbs;
 
 if (clSeq != NULL)
     {
     char seqSpec[2*PATH_LEN];