838bd75e5d5b859f5b81102933273b7c7e7e2114 markd Sun Aug 16 10:29:38 2020 -0700 removed redundent function diff --git src/hg/inc/genePred.h src/hg/inc/genePred.h index bba40c1..cf62880 100644 --- src/hg/inc/genePred.h +++ src/hg/inc/genePred.h @@ -280,30 +280,38 @@ * optional fields that preceed the highest optFields column. chromIndexLen * is now ignored.. */ struct genePred *getOverlappingGene(char *db, struct genePred **list, char *table, char *chrom, int cStart, int cEnd, char *name, int *retOverlap); /* read all genes from a table find the gene with the biggest overlap. * Cache the list of genes to so we only read it once. * If there are multiple hits and the name that matches exactly, * this overrides the biggest overlap */ int genePredBases(struct genePred *gp); /* count coding and utr bases in a gene prediction */ int genePredCodingBases(struct genePred *gp); /* Count up the number of coding bases in gene prediction. */ +INLINE int genePredCdsSize(struct genePred *gp) +/* Count up the number of coding bases in gene prediction. + * This function is redundant. */ +{ +return genePredCodingBases(gp); +} + + boolean genePredCdsExon(struct genePred *gp, int iExon, int *startPtr, int *endPtr); /* Get the CDS range in an exon. If there is no CDS, return FALSE and then * set start == end */ int genePredCheck(char *desc, FILE* errFh, int chromSize, struct genePred* gp); /* Validate a genePred for consistency. desc is printed the error messages * to file errFh (open /dev/null to discard). chromSize should contain * size of chromosome, or 0 if chrom is not valid, or -1 to not check * chromosome bounds. Returns count of errors. */ int genePredCheckDb(char *desc, FILE* errFh, char* db, struct genePred* gp); /* Validate a genePred for consistency. desc is printed the error messages * to file errFh (open /dev/null to discard). Lookup chromosome size in database if * db is not NULL. Returns count of errors. */ @@ -315,33 +323,30 @@ */ boolean genePredNmdTarget(struct genePred *gp); /* Return TRUE if cds end is more than 50bp upstream of last intron. */ void genePredAddExonFrames(struct genePred *gp); /* Add exonFrames array to a genePred that doesn't have it. Frame is assumed * to be contiguous. */ void genePredRc(struct genePred *gp, int chromSize); /* Reverse complement a genePred (project it to the opposite strand). Useful * when doing analysis that is simplified by having things on the same strand. */ -int genePredCdsSize(struct genePred *gp); -/* compute the number of bases of CDS */ - struct genePred *genePredNew(char *name, char *chrom, char strand, unsigned txStart, unsigned txEnd, unsigned cdsStart, unsigned cdsEnd, unsigned optFields, unsigned exonSpace); /* create a new gene with space for the specified number of exons allocated. * genePredGrow maybe used to expand this space if needed. */ void genePredGrow(struct genePred *gp, unsigned *exonSpacePtr); /* Increase memory allocated to a psl to hold more exons. exonSpacePtr * should point the the current maximum number of exons and will be * updated to with the new amount of space. */ struct rbTree *genePredToRangeTree(struct genePred *gp, boolean cdsOnly); /* Convert genePred into a range tree. */