83ccf1c6b15c91b83723894b882f3af1e340882b
braney
  Sun Jun 1 16:37:23 2025 -0700
exon frames are in transcription strand order so if it's changed during quickLift we need to flip the order in the genePred

diff --git src/hg/inc/genePred.h src/hg/inc/genePred.h
index cf0e3cbe84a..c25292cfea1 100644
--- src/hg/inc/genePred.h
+++ src/hg/inc/genePred.h
@@ -400,21 +400,21 @@
 
 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);
+struct genePredExt  *genePredFromBedBigGenePred( char *chrom, struct bed *bed, struct bigBedInterval *bb, boolean changedStrand);
 /* build a genePred from a bigGenePred and a bed file */
 
 struct genePred *genePredExtLoad15(char **row);
 /* Load a genePred record assumed to be 15 fields. */
 #endif /* GENEPRED_H */