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
@@ -1,83 +1,85 @@
 /* bigGenePred.h was originally generated by the autoSql program, which also 
  * generated bigGenePred.c and bigGenePred.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef BIGGENEPRED_H
 #define BIGGENEPRED_H
 
 #define BIGGENEPRED_NUM_COLS 20
 
 #include "genePred.h"
 #include "asParse.h"
 
 extern char *bigGenePredCommaSepFieldNames;
 
 struct bigGenePred
 /* bigGenePred gene models */
     {
     struct bigGenePred *next;  /* Next in singly linked list. */
     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);
 /* Load all bigGenePred from chopper separated file.
  * Dispose of this with bigGenePredFreeList(). */
 
 #define bigGenePredLoadAllByTab(a) bigGenePredLoadAllByChar(a, '\t');
 /* Load all bigGenePred from tab separated file.
  * Dispose of this with bigGenePredFreeList(). */
 
 struct bigGenePred *bigGenePredCommaIn(char **pS, struct bigGenePred *ret);
 /* Create a bigGenePred out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bigGenePred */
 
 void bigGenePredFree(struct bigGenePred **pEl);
 /* Free a single dynamically allocated bigGenePred such as created
  * with bigGenePredLoad(). */
 
 void bigGenePredFreeList(struct bigGenePred **pList);
 /* Free a list of dynamically allocated bigGenePred's */
 
 void bigGenePredOutput(struct bigGenePred *el, FILE *f, char sep, char lastSep);
 /* Print out bigGenePred.  Separate fields with sep. Follow last field with lastSep. */
 
 #define bigGenePredTabOut(el,f) bigGenePredOutput(el,f,'\t','\n');
 /* Print out bigGenePred as a line in a tab-separated file. */
 
 #define bigGenePredCommaOut(el,f) bigGenePredOutput(el,f,',',',');
 /* Print out bigGenePred as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct asObject *bigGenePredAsObj();
 // Return asObject describing fields of bigGenePred
 
 #endif /* BIGGENEPRED_H */