c1e66c5c9d45f0965156318e2782714ee93b04ab
braney
  Mon Oct 19 16:08:32 2015 -0700
more work on bigMaf.  Works in hgc and hgTables now.  #15935

diff --git src/hg/inc/hgMaf.h src/hg/inc/hgMaf.h
index 49eb9db..d6c4a8d 100644
--- src/hg/inc/hgMaf.h
+++ src/hg/inc/hgMaf.h
@@ -1,26 +1,27 @@
 /* hgMaf.h - Stuff to load up mafs from the browser database.
  *           Also, items for maf track display */
 
 /* Copyright (C) 2012 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 #ifndef HGMAF_H
 #define HGMAF_H
 
 
 #include "trackDb.h"
 #include "cart.h"
+#include "bbiFile.h"
 
 /* Track settings and variables */
 #define SPECIES_TREE_VAR        "speciesTree"
 #define SPECIES_ORDER_VAR       "speciesOrder"
 #define SPECIES_GROUP_VAR       "speciesGroups"
 #define SPECIES_TARGET_VAR      "speciesTarget"
 #define SPECIES_DEFAULT_OFF_VAR "speciesDefaultOff"
 #define SPECIES_GROUP_PREFIX    "sGroup_"
 #define SPECIES_HTML_TARGET	"sT"
 #define SPECIES_CODON_DEFAULT	"speciesCodonDefault"
 #define SPECIES_USE_FILE        "speciesUseFile"
 #define PAIRWISE_VAR            "pairwise"
 #define PAIRWISE_HEIGHT         "pairwiseHeight"
 #define SUMMARY_VAR             "summary"
 #define BASE_COLORS_VAR         "baseColors"
@@ -87,16 +88,19 @@
     {
     struct wigMafSpecies *next;
     char *name;
     int group;
     boolean on;
     };
 
 struct wigMafSpecies * wigMafSpeciesTable(struct cart *cart,
     struct trackDb *tdb, char *name, char *db) ;
 char **wigMafGetSpecies(struct cart *cart, struct trackDb *tdb, char *prefix, char *db, 
                         struct wigMafSpecies **list, int *groupCt);
 
 struct consWiggle *consWiggleFind(char *db,struct trackDb *parent,char *table);
 /* Return conservation wig if it is found in the parent. */
 
+struct mafAli *bigMafLoadInRegion( struct bbiFile *bbi, char *chrom, int start, int end);
+/* Read in MAF blocks from bigBed. */
+
 #endif//ndef HGMAF_H