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/hapmapSnps.h src/hg/inc/hapmapSnps.h
index a4e4199..0d5ee1d 100644
--- src/hg/inc/hapmapSnps.h
+++ src/hg/inc/hapmapSnps.h
@@ -1,109 +1,109 @@
 /* hapmapSnps.h was originally generated by the autoSql program, which also 
  * generated hapmapSnps.c and hapmapSnps.sql.  This header links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2009 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 HAPMAPSNPS_H
 #define HAPMAPSNPS_H
 
 #define HAPMAPSNPS_NUM_COLS 12
 
 struct hapmapSnps
 /* HapMap genotype summary */
     {
     struct hapmapSnps *next;  /* Next in singly linked list. */
     char *chrom;	/* Chromosome */
     unsigned chromStart;	/* Start position in chrom (0 based) */
     unsigned chromEnd;	/* End position in chrom (1 based) */
     char *name;	/* Reference SNP identifier from dbSnp */
     unsigned score;	/* Not used */
     char strand[2];	/* Which genomic strand contains the observed alleles */
     char *observed;	/* Observed string from genotype file */
     char allele1[2];	/* This allele has been observed */
     unsigned homoCount1;	/* Count of individuals who are homozygous for allele1 */
     char *allele2;	/* This allele may not have been observed */
     unsigned homoCount2;	/* Count of individuals who are homozygous for allele2 */
     unsigned heteroCount;	/* Count of individuals who are heterozygous */
     };
 
 void hapmapSnpsStaticLoad(char **row, struct hapmapSnps *ret);
 /* Load a row from hapmapSnps table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct hapmapSnps *hapmapSnpsLoad(char **row);
 /* Load a hapmapSnps from row fetched with select * from hapmapSnps
  * from database.  Dispose of this with hapmapSnpsFree(). */
 
 struct hapmapSnps *hapmapSnpsLoadAll(char *fileName);
 /* Load all hapmapSnps from whitespace-separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 
 struct hapmapSnps *hapmapSnpsLoadAllByChar(char *fileName, char chopper);
 /* Load all hapmapSnps from chopper separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 
 #define hapmapSnpsLoadAllByTab(a) hapmapSnpsLoadAllByChar(a, '\t');
 /* Load all hapmapSnps from tab separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 
 struct hapmapSnps *hapmapSnpsCommaIn(char **pS, struct hapmapSnps *ret);
 /* Create a hapmapSnps out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapSnps */
 
 void hapmapSnpsFree(struct hapmapSnps **pEl);
 /* Free a single dynamically allocated hapmapSnps such as created
  * with hapmapSnpsLoad(). */
 
 void hapmapSnpsFreeList(struct hapmapSnps **pList);
 /* Free a list of dynamically allocated hapmapSnps's */
 
 void hapmapSnpsOutput(struct hapmapSnps *el, FILE *f, char sep, char lastSep);
 /* Print out hapmapSnps.  Separate fields with sep. Follow last field with lastSep. */
 
 #define hapmapSnpsTabOut(el,f) hapmapSnpsOutput(el,f,'\t','\n');
 /* Print out hapmapSnps as a line in a tab-separated file. */
 
 #define hapmapSnpsCommaOut(el,f) hapmapSnpsOutput(el,f,',',',');
 /* Print out hapmapSnps as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 /* items for trackUi options and filters */
 
 #define HAP_POP_MIXED "hapmapSnps_isMixed"
 #define HAP_POP_COUNT "hapmapSnps_popCount"
 #define HAP_TYPE "hapmapSnps_polyType"
 #define HAP_MIN_FREQ "hapmapSnps_minorAlleleFreqMinimum"
 #define HAP_MAX_FREQ "hapmapSnps_minorAlleleFreqMaximum"
 #define HAP_MIN_HET "hapmapSnps_hetMinimum"
 #define HAP_MAX_OBSERVED_HET "hapmapSnps_obsHetMaximum"
 #define HAP_MAX_EXPECTED_HET "hapmapSnps_expHetMaximum"
 #define HAP_MONO_PREFIX "hapmapSnps_monomorphic"
 #define HAP_ORTHO_PREFIX "hapmapSnps_ortho"
 #define HAP_ORTHO_QUAL_PREFIX "hapmapSnps_orthoQual"
 
 #define HAP_FILTER_DEFAULT "no filter"
 
 #define HAP_MIN_FREQ_DEFAULT  "0.0"
 #define HAP_MAX_FREQ_DEFAULT  "0.5"
 #define HAP_MIN_HET_DEFAULT   "0.0"
 #define HAP_MAX_EXPECTED_HET_DEFAULT   "0.5"
 #define HAP_MAX_OBSERVED_HET_DEFAULT   "1.0"
 
 #define HAP_ORTHO_QUAL_DEFAULT "0"
 
 #define HAP_PHASEII_POPCOUNT 4
 #define HAP_PHASEIII_POPCOUNT 11
 #define HAP_ORTHO_COUNT 2
 
 extern char *hapmapPhaseIIPops[HAP_PHASEII_POPCOUNT];
 extern char *hapmapPhaseIIIPops[HAP_PHASEIII_POPCOUNT];
 
 /* Someday this should come from a trackDb setting: */
 extern char *hapmapOrthoSpecies[HAP_ORTHO_COUNT+1];
 
 #endif /* HAPMAPSNPS_H */