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/cgilib/gwasCatalog.c src/hg/cgilib/gwasCatalog.c
index 1e2959a..0f1c53f 100644
--- src/hg/cgilib/gwasCatalog.c
+++ src/hg/cgilib/gwasCatalog.c
@@ -1,280 +1,280 @@
 /* gwasCatalog.c was originally generated by the autoSql program, which also 
  * generated gwasCatalog.h and gwasCatalog.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 "gwasCatalog.h"
 
 
 /* definitions for cnv column */
 static char *values_cnv[] = {"Y", "N", NULL};
 static struct hash *valhash_cnv = NULL;
 
 void gwasCatalogStaticLoad(char **row, struct gwasCatalog *ret)
 /* Load a row from gwasCatalog 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->pubMedID = sqlUnsigned(row[4]);
 ret->author = row[5];
 ret->pubDate = row[6];
 ret->journal = row[7];
 ret->title = row[8];
 ret->trait = row[9];
 ret->initSample = row[10];
 ret->replSample = row[11];
 ret->region = row[12];
 ret->genes = row[13];
 ret->riskAllele = row[14];
 ret->riskAlFreq = row[15];
 ret->pValue = row[16];
 ret->pValueDesc = row[17];
 ret->orOrBeta = row[18];
 ret->ci95 = row[19];
 ret->platform = row[20];
 ret->cnv = sqlEnumParse(row[21], values_cnv, &valhash_cnv);
 }
 
 struct gwasCatalog *gwasCatalogLoad(char **row)
 /* Load a gwasCatalog from row fetched with select * from gwasCatalog
  * from database.  Dispose of this with gwasCatalogFree(). */
 {
 struct gwasCatalog *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->pubMedID = sqlUnsigned(row[4]);
 ret->author = cloneString(row[5]);
 ret->pubDate = cloneString(row[6]);
 ret->journal = cloneString(row[7]);
 ret->title = cloneString(row[8]);
 ret->trait = cloneString(row[9]);
 ret->initSample = cloneString(row[10]);
 ret->replSample = cloneString(row[11]);
 ret->region = cloneString(row[12]);
 ret->genes = cloneString(row[13]);
 ret->riskAllele = cloneString(row[14]);
 ret->riskAlFreq = cloneString(row[15]);
 ret->pValue = cloneString(row[16]);
 ret->pValueDesc = cloneString(row[17]);
 ret->orOrBeta = cloneString(row[18]);
 ret->ci95 = cloneString(row[19]);
 ret->platform = cloneString(row[20]);
 ret->cnv = sqlEnumParse(row[21], values_cnv, &valhash_cnv);
 return ret;
 }
 
 struct gwasCatalog *gwasCatalogLoadAll(char *fileName) 
 /* Load all gwasCatalog from a whitespace-separated file.
  * Dispose of this with gwasCatalogFreeList(). */
 {
 struct gwasCatalog *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileRow(lf, row))
     {
     el = gwasCatalogLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gwasCatalog *gwasCatalogLoadAllByChar(char *fileName, char chopper) 
 /* Load all gwasCatalog from a chopper separated file.
  * Dispose of this with gwasCatalogFreeList(). */
 {
 struct gwasCatalog *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gwasCatalogLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gwasCatalog *gwasCatalogCommaIn(char **pS, struct gwasCatalog *ret)
 /* Create a gwasCatalog out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gwasCatalog */
 {
 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->pubMedID = sqlUnsignedComma(&s);
 ret->author = sqlStringComma(&s);
 ret->pubDate = sqlStringComma(&s);
 ret->journal = sqlStringComma(&s);
 ret->title = sqlStringComma(&s);
 ret->trait = sqlStringComma(&s);
 ret->initSample = sqlStringComma(&s);
 ret->replSample = sqlStringComma(&s);
 ret->region = sqlStringComma(&s);
 ret->genes = sqlStringComma(&s);
 ret->riskAllele = sqlStringComma(&s);
 ret->riskAlFreq = sqlStringComma(&s);
 ret->pValue = sqlStringComma(&s);
 ret->pValueDesc = sqlStringComma(&s);
 ret->orOrBeta = sqlStringComma(&s);
 ret->ci95 = sqlStringComma(&s);
 ret->platform = sqlStringComma(&s);
 ret->cnv = sqlEnumComma(&s, values_cnv, &valhash_cnv);
 *pS = s;
 return ret;
 }
 
 void gwasCatalogFree(struct gwasCatalog **pEl)
 /* Free a single dynamically allocated gwasCatalog such as created
  * with gwasCatalogLoad(). */
 {
 struct gwasCatalog *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->author);
 freeMem(el->pubDate);
 freeMem(el->journal);
 freeMem(el->title);
 freeMem(el->trait);
 freeMem(el->initSample);
 freeMem(el->replSample);
 freeMem(el->region);
 freeMem(el->genes);
 freeMem(el->riskAllele);
 freeMem(el->riskAlFreq);
 freeMem(el->pValue);
 freeMem(el->pValueDesc);
 freeMem(el->orOrBeta);
 freeMem(el->ci95);
 freeMem(el->platform);
 freez(pEl);
 }
 
 void gwasCatalogFreeList(struct gwasCatalog **pList)
 /* Free a list of dynamically allocated gwasCatalog's */
 {
 struct gwasCatalog *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gwasCatalogFree(&el);
     }
 *pList = NULL;
 }
 
 void gwasCatalogOutput(struct gwasCatalog *el, FILE *f, char sep, char lastSep) 
 /* Print out gwasCatalog.  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->pubMedID);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->author);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pubDate);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->journal);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->title);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->trait);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->initSample);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->replSample);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->region);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genes);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->riskAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->riskAlFreq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pValue);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pValueDesc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orOrBeta);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ci95);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->platform);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->cnv, values_cnv);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */