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/genePred.h src/hg/inc/genePred.h
index 6eb2c54..5070682 100644
--- src/hg/inc/genePred.h
+++ src/hg/inc/genePred.h
@@ -81,33 +81,34 @@
     unsigned cdsStart;	/* Coding region start */
     unsigned cdsEnd;	/* Coding region end */
     unsigned exonCount;	/* Number of exons */
     unsigned *exonStarts;	/* Exon start positions */
     unsigned *exonEnds;	/* Exon end positions */
 
     /* optional fields */
     unsigned optFields;           /* which optional fields are used (not in
                                    * database) */
     int score;                    /* score */
     char *name2;                  /* Secondary name. (e.g. name of gene), or
                                    * empty if none, NULL if field not
                                    * requested */
     enum cdsStatus cdsStartStat;  /* Status of cdsStart annotation */
     enum cdsStatus cdsEndStat;    /* Status of cdsEnd annotation */
-    int *exonFrames;              /* List of frame for each exon, or -1
-                                   * if no frame or not known. NULL if not
-                                   * available. */
+    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.
+                                   * NULL if not available */
     char *type;
     char *geneName;  
     char *geneName2;
     char *geneType;
 };
 
 struct genePred
 /* A gene prediction, with optional fields. */
 {
     struct genePred *next;  /* Next in singly linked list. */
     char *name;	/* Name of loci, transcript, mRNA, etc */
     char *chrom;	/* Chromosome name */
     char strand[2];	/* + or - for strand */
     unsigned txStart;	/* Transcription start position */
     unsigned txEnd;	/* Transcription end position */