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);