4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index fc000d6..5a2cd65 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -1,87 +1,87 @@
 /* gpFx --- routines to calculate the effect of variation on a genePred; variantProjector.c can
  * also produce struct gpFx results using PSL+CDS+sequence, more accurate than genePred. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef GPFX_H
 #define GPFX_H
 
 #include "variant.h"
 #include "soTerm.h"
 
 // a single gpFx variant effect call
 struct gpFx
     {
     struct gpFx *next;
     char *gAllele;		// Genomic allele sequence used to determine functional effect
     char *transcript;		// ID of feature affected by this call
     uint soNumber;		// Sequence Ontology Number of effect
     enum detailType		// This tells which value to use for 'union details' below
 	{
 	unknown,		// Catch uninitialized (except for needMem) use
 	codingChange,		// (non)synonymous variant, deletions in CDS
 	nonCodingExon,		// variant in non-coding gene or UTR of coding gene
 	intron,			// intron_variant
 	none			// variant for which soNumber is enough (e.g. up/downstream)
 	} detailType;
     union details
 	{
 	struct codingChange     // (non)synonymous variant, deletions in CDS
 	    {
 	    uint exonNumber;	// 0-based exon number (from genePred, beware false "introns")
             uint exonCount;     // Total number of exons (sometimes less than aligned blocks)
 	    uint cDnaPosition;	// offset of variant in transcript cDNA
 	    char *txRef;	// Transcript reference allele (usually == genomic ref % strand)
 	    char *txAlt;	// Transcript alternate allele (usually == gAllele % strand)
 	    uint cdsPosition;	// offset of variant from transcript's cds start
 	    uint pepPosition;	// offset of variant in translated product
 	    char *aaOld;	// peptides, before change by variant (starting at pepPos)
 	    char *aaNew;	// peptides, changed by variant
 	    char *codonOld;	// codons, before change by variant (starting at cdsPos)
 	    char *codonNew;	// codons, changed by variant
 	    } codingChange;
 	struct nonCodingExon	// variant in non-coding gene or UTR of coding gene
 	    {
 	    uint exonNumber;	// 0-based exon number (from genePred, beware false "introns")
             uint exonCount;     // Total number of exons (sometimes less than aligned blocks)
 	    uint cDnaPosition;	// offset of variant in transcript cDNA
 	    char *txRef;	// Transcript reference allele (usually == genomic ref % strand)
 	    char *txAlt;	// Transcript alternate allele (usually == gAllele % strand)
 	    } nonCodingExon;
 	struct intron 		// intron_variant
 	    {
 	    uint intronNumber;	// 0-based intron number (from genePred, beware false "introns")
             uint intronCount;   // Total number of introns (sometimes less than aligned blocks - 1)
 	    } intron;
 	} details;
     };
 
 struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,
 			    struct dnaSeq *transcriptSequence, struct lm *lm);
 // return the predicted effect(s) of a variation list on a genePred
 
 // number of bases up or downstream that we flag
 #define GPRANGE 5000
 
 boolean hasAltAllele(struct allele *alleles);
 /* Return TRUE if alleles include at least one non-reference allele. */
 
 char *firstAltAllele(struct allele *alleles);
 /* Ensembl always reports an alternate allele, even if that allele is not being used
  * to calculate any consequence.  When allele doesn't really matter, just use the
  * first alternate allele that is given. */
 
 struct gpFx *gpFxNew(char *gAllele, char *transcript, enum soTerm soNumber,
 		     enum detailType detailType, struct lm *lm);
 /* Fill in the common members of gpFx; leave soTerm-specific members for caller to fill in. */
 
 struct gpFx *gpFxNoVariation(struct variant *variant, struct lm *lm);
 /* Return a gpFx with SO term no_sequence_alteration, for VCF rows that aren't really variants. */
 
 void gpFxSetNoncodingInfo(struct gpFx *gpFx, int exonIx, int exonCount, int cdnaPos,
                           char *txRef, char *txAlt, struct lm *lm);
 /* This gpFx is for a variant in exon of non-coding gene or UTR exon of coding gene;
  * set details.nonCodingExon values. */
 
 #endif /* GPFX_H */