13b584581e6d7b1860e0cab97adc3594b1899308
braney
  Mon Aug 7 12:05:10 2023 -0700
add instaPort to bigBed support

diff --git src/hg/inc/genePred.h src/hg/inc/genePred.h
index 329a6da..6eb2c54 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 kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef GENEPRED_H
 #define GENEPRED_H
 
 #include "dnaseq.h"
+#include "basicBed.h"
 #include "bigBed.h"
 #include "nibTwo.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)  */
@@ -398,16 +399,18 @@
 
 void genePredTranslate(struct genePred *gp, struct nibTwoCache* genomeSeqs, unsigned options,
                        char **protRet, char **cdsRet);
 /* Translate a genePred into a protein.  It can also return the CDS part of the
  * mRNA sequence. If the chrom is chrM, the mitochondrial translation tables are
  * used. If protRet or cdsRet is NULL, those sequences are not returned.
  */
 
 void genePredToCds(struct genePred *gp, struct genbankCds *cds);
 /* Fill in cds with transcript offsets computed from genePred. */
 
 struct psl *genePredToPsl(struct genePred *gp, int chromSize, int qSize);
 /* Convert a genePred to psl, assuming perfect concordance between target & query.
  * If qSize is 0 then the number of aligned bases will be used as qSize. */
 
+struct genePredExt  *genePredFromBedBigGenePred( char *chrom, struct bed *bed, struct bigBedInterval *bb);
+/* build a genePred from a bigGenePred and a bed file */
 #endif /* GENEPRED_H */