c84cfb3709fec4c63ae72505aba7cc32dd359039
braney
  Mon Jan 16 11:41:46 2017 -0800
add maskBed option to twoBitInfo to get a bed file of masked regions

diff --git src/inc/twoBit.h src/inc/twoBit.h
index ecf1172..85394db 100644
--- src/inc/twoBit.h
+++ src/inc/twoBit.h
@@ -190,30 +190,33 @@
  *
  * free result with twoBitSpecFree().
  */
 
 struct twoBitSpec *twoBitSpecNewFile(char *twoBitFile, char *specFile);
 /* parse a file containing a list of specifications for sequences in the
  * specified twoBit file. Specifications are one per line in forms:
  *     seqName
  *  or
  *     seqName:start-end
  */
 
 void twoBitSpecFree(struct twoBitSpec **specPtr);
 /* free a twoBitSpec object */
 
+void twoBitOutMaskBeds(struct twoBitFile *tbf, char *seqName, FILE *outF);
+/* output a series of bed3's that enumerate the number of masked bases in a sequence*/
+
 void twoBitOutNBeds(struct twoBitFile *tbf, char *seqName, FILE *outF);
 /* output a series of bed3's that enumerate the number of N's in a sequence*/
 
 int twoBitSeqSizeNoNs(struct twoBitFile *tbf, char *seqName);
 /* return the length of the sequence, not counting N's */
 
 long long twoBitTotalSizeNoN(struct twoBitFile *tbf);
 /* return the size of the all the sequence in file, not counting N's*/
 
 boolean twoBitIsSequence(struct twoBitFile *tbf, char *chromName);
 /* Return TRUE if chromName is in 2bit file. */
 
 struct hash *twoBitChromHash(char *fileName);
 /* Build a hash of chrom names with their sizes. */
 #endif /* TWOBIT_H */