6c16a029709c60f4d88f5a2a01ef7422c78c89c4
braney
  Fri Sep 19 15:30:36 2014 -0700
show SNPs as red in maf and wigMaf tracks if "showSnp on" is set in the trackDb
diff --git src/inc/maf.h src/inc/maf.h
index d337958..3e3f06b 100644
--- src/inc/maf.h
+++ src/inc/maf.h
@@ -213,30 +213,36 @@
 
 double mafScoreMultiz(struct mafAli *maf);
 /* Return score of a maf (calculated rather than what is
  * stored in the structure. */
 
 double mafScoreRangeMultiz(struct mafAli *maf, int start, int size);
 /* Return score of a subset of an alignment.  Parameters are:
  *    maf - the alignment
  *    start - the (zero based) offset to start calculating score
  *    size - the size of the subset
  * The following relationship should hold:
  *   scoreRange(maf,start,size) =
  *	scoreRange(maf,0,start+size) - scoreRange(maf,0,start)
  */
 
+void mafScoreUseSimple();
+/* use a simple scoring system useful for finding mismatches */
+
+void mafScoreUseTraditional();
+/* use the tradition HOX scoring system */
+
 double mafScoreMultizMaxCol(int species);
 /* Return maximum possible score for a column. */
 
 void mafColMinMaxScore(struct mafAli *maf, 
 	double *retMin, double *retMax);
 /* Get min/max maf scores for a column. */
 
 void mafFlipStrand(struct mafAli *maf);
 /* Reverse complement maf. */
 
 void mafSrcDb(char *name, char *retDb, int retDbSize);
 /* Parse out just database part of name (up to but not including
  * first dot). If dot found, return entire name */
 
 boolean mafColumnEmpty(struct mafAli *maf, int col);