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/lib/orthoAlleles.c src/hg/lib/orthoAlleles.c
index 41fcf70..4d9f651 100644
--- src/hg/lib/orthoAlleles.c
+++ src/hg/lib/orthoAlleles.c
@@ -1,248 +1,248 @@
 /* orthoAlleles.c was originally generated by the autoSql program, which also 
  * generated orthoAlleles.h and orthoAlleles.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 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. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "orthoAlleles.h"
 
 
 void orthoAllelesStaticLoad(char **row, struct orthoAlleles *ret)
 /* Load a row from orthoAlleles table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 ret->strand = row[5][0];
 ret->allele1 = row[6][0];
 ret->allele1Freq = atof(row[7]);
 ret->allele1Count = sqlUnsigned(row[8]);
 ret->allele2 = row[9][0];
 ret->allele2Freq = atof(row[10]);
 ret->allele2Count = sqlUnsigned(row[11]);
 ret->ortho1Chrom = row[12];
 ret->ortho1ChromStart = sqlUnsigned(row[13]);
 ret->ortho1ChromEnd = sqlUnsigned(row[14]);
 ret->ortho1Strand = row[15][0];
 ret->ortho1State = row[16];
 ret->ortho2Chrom = row[17];
 ret->ortho2ChromStart = sqlUnsigned(row[18]);
 ret->ortho2ChromEnd = sqlUnsigned(row[19]);
 ret->ortho2Strand = row[20][0];
 ret->ortho2State = row[21];
 }
 
 struct orthoAlleles *orthoAllelesLoad(char **row)
 /* Load a orthoAlleles from row fetched with select * from orthoAlleles
  * from database.  Dispose of this with orthoAllelesFree(). */
 {
 struct orthoAlleles *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 ret->strand = row[5][0];
 ret->allele1 = row[6][0];
 ret->allele1Freq = atof(row[7]);
 ret->allele1Count = sqlUnsigned(row[8]);
 ret->allele2 = row[9][0];
 ret->allele2Freq = atof(row[10]);
 ret->allele2Count = sqlUnsigned(row[11]);
 ret->ortho1Chrom = cloneString(row[12]);
 ret->ortho1ChromStart = sqlUnsigned(row[13]);
 ret->ortho1ChromEnd = sqlUnsigned(row[14]);
 ret->ortho1Strand = row[15][0];
 ret->ortho1State = cloneString(row[16]);
 ret->ortho2Chrom = cloneString(row[17]);
 ret->ortho2ChromStart = sqlUnsigned(row[18]);
 ret->ortho2ChromEnd = sqlUnsigned(row[19]);
 ret->ortho2Strand = row[20][0];
 ret->ortho2State = cloneString(row[21]);
 return ret;
 }
 
 struct orthoAlleles *orthoAllelesLoadAll(char *fileName) 
 /* Load all orthoAlleles from a whitespace-separated file.
  * Dispose of this with orthoAllelesFreeList(). */
 {
 struct orthoAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileRow(lf, row))
     {
     el = orthoAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct orthoAlleles *orthoAllelesLoadAllByChar(char *fileName, char chopper) 
 /* Load all orthoAlleles from a chopper separated file.
  * Dispose of this with orthoAllelesFreeList(). */
 {
 struct orthoAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = orthoAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct orthoAlleles *orthoAllelesCommaIn(char **pS, struct orthoAlleles *ret)
 /* Create a orthoAlleles out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new orthoAlleles */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->strand), sizeof(ret->strand));
 sqlFixedStringComma(&s, &(ret->allele1), sizeof(ret->allele1));
 ret->allele1Freq = sqlFloatComma(&s);
 ret->allele1Count = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->allele2), sizeof(ret->allele2));
 ret->allele2Freq = sqlFloatComma(&s);
 ret->allele2Count = sqlUnsignedComma(&s);
 ret->ortho1Chrom = sqlStringComma(&s);
 ret->ortho1ChromStart = sqlUnsignedComma(&s);
 ret->ortho1ChromEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->ortho1Strand), sizeof(ret->ortho1Strand));
 ret->ortho1State = sqlStringComma(&s);
 ret->ortho2Chrom = sqlStringComma(&s);
 ret->ortho2ChromStart = sqlUnsignedComma(&s);
 ret->ortho2ChromEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->ortho2Strand), sizeof(ret->ortho2Strand));
 ret->ortho2State = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void orthoAllelesFree(struct orthoAlleles **pEl)
 /* Free a single dynamically allocated orthoAlleles such as created
  * with orthoAllelesLoad(). */
 {
 struct orthoAlleles *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->ortho1Chrom);
 freeMem(el->ortho1State);
 freeMem(el->ortho2Chrom);
 freeMem(el->ortho2State);
 freez(pEl);
 }
 
 void orthoAllelesFreeList(struct orthoAlleles **pList)
 /* Free a list of dynamically allocated orthoAlleles's */
 {
 struct orthoAlleles *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     orthoAllelesFree(&el);
     }
 *pList = NULL;
 }
 
 void orthoAllelesOutput(struct orthoAlleles *el, FILE *f, char sep, char lastSep) 
 /* Print out orthoAlleles.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->allele1);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->allele1Freq);
 fputc(sep,f);
 fprintf(f, "%u", el->allele1Count);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->allele2);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->allele2Freq);
 fputc(sep,f);
 fprintf(f, "%u", el->allele2Count);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ortho1Chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->ortho1ChromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->ortho1ChromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->ortho1Strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ortho1State);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ortho2Chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->ortho2ChromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->ortho2ChromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->ortho2Strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ortho2State);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */