440d84ee43c6a5f8a22bfe7886681db4ee7cc202
braney
  Thu Aug 28 16:55:27 2014 -0700
adding more support for bigGenePred in hgc and hgTables.
diff --git src/hg/inc/genePred.h src/hg/inc/genePred.h
index 0da9c58..2423b13 100644
--- src/hg/inc/genePred.h
+++ src/hg/inc/genePred.h
@@ -1,26 +1,27 @@
 /* genePred.h was originally generated by the autoSql program, which also 
  * generated genePred.c and genePred.sql.  This header links the database and the RAM 
  * representation of objects. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #ifndef GENEPRED_H
 #define GENEPRED_H
 
 #include "dnaseq.h"
+#include "bigBed.h"
 
 struct gff;
 struct gffFile;
 struct gffGroup;
 struct psl;
 struct genbankCds;
 struct rbTree;
 
 enum cdsStatus
 /* value to indicate status of CDS annotation at either start or end */
 {
     cdsNone,        /* "none" - No CDS (non-coding)  */
     cdsUnknown,     /* "unk" - CDS is unknown (coding, but not known)  */
     cdsIncomplete,  /* "incmpl" - CDS is not complete at this end  */
     cdsComplete,    /* "cmpl" - CDS is complete at this end  */
@@ -307,17 +308,19 @@
 // Return asObject describing fields of genePred
 
 struct dnaSeq *genePredGetDna(char *database, struct genePred *gp,
                               boolean coding, enum dnaCase dnaCase);
 // Returns the DNA sequence associated with gene prediction.
 // Negative strand genes will return the sequence as read from the negative strand.
 // Optionally restrict to coding sequence only
 
 int genePredBaseToCodingPos(struct genePred *gp, int basePos,
                             boolean stranded, boolean *isCoding);
 // Given a genePred model and a single (0 based) base position, predict the 0-based
 // DNA (stranded) coding sequence pos.  Dividing this number by 3 should give the AA position!
 // Returns -1 when outside of coding exons unless OPTIONAL isCoding pointer to boolean is
 // provided. In that case, returns last valid position and sets isCoding to FALSE.
 
+struct genePred  *genePredFromBigGenePred( char *chrom, struct bigBedInterval *bb);
+/* build a genePred from a bigGenePred */
 #endif /* GENEPRED_H */