0ca882d44fa40a7437a84dc68bf0c0774fc23785
markd
  Mon Nov 27 09:58:06 2023 -0800
update autoSql documentation to better describe exonFrames in genePredExt and bigGenePred

diff --git src/hg/inc/bigGenePred.h src/hg/inc/bigGenePred.h
index ae4ad70..5938d03 100644
--- src/hg/inc/bigGenePred.h
+++ src/hg/inc/bigGenePred.h
@@ -19,31 +19,33 @@
     char *chrom;	/* Reference sequence chromosome or scaffold */
     unsigned chromStart;	/* Start position in chromosome */
     unsigned chromEnd;	/* End position in chromosome */
     char *name;	/* Name or ID of item, ideally both human readable and unique */
     unsigned score;	/* Score (0-1000) */
     char strand[2];	/* + or - for strand */
     unsigned thickStart;	/* Start of where display should be thick (start codon) */
     unsigned thickEnd;	/* End of where display should be thick (stop codon) */
     unsigned itemRgb;	/* RGB value (use R,G,B string in input file) */
     unsigned blockCount;	/* Number of blocks */
     unsigned *blockSizes;	/* Comma separated list of block sizes */
     unsigned *chromStarts;	/* Start positions relative to chromStart */
     char *name2;	/* Alternative/human readable name */
     enum cdsStatus  cdsStartStat;	/* enum('none','unk','incmpl','cmpl') */
     enum cdsStatus cdsEndStat;	/* enum('none','unk','incmpl','cmpl') */
-    int *exonFrames;	/* Exon frame {0,1,2}, or -1 if no frame for exon */
+    int *exonFrames;	/* Reading frame of the start of the CDS region of the exon,
+                         * in the direction of transcription (0,1,2), or -1 if there
+                         * is no CDS region. */
     char *type;	/* Transcript type */
     char *geneName;	/* Primary identifier for gene */
     char *geneName2;	/* Alternative/human readable gene name */
     char *geneType;	/* Gene type */
     };
 
 struct bigGenePred *bigGenePredLoad(char **row);
 /* Load a bigGenePred from row fetched with select * from bigGenePred
  * from database.  Dispose of this with bigGenePredFree(). */
 
 struct bigGenePred *bigGenePredLoadAll(char *fileName);
 /* Load all bigGenePred from whitespace-separated file.
  * Dispose of this with bigGenePredFreeList(). */
 
 struct bigGenePred *bigGenePredLoadAllByChar(char *fileName, char chopper);