533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/lib/gwasCatalog.c src/hg/lib/gwasCatalog.c
deleted file mode 100644
index 1e2959a..0000000
--- src/hg/lib/gwasCatalog.c
+++ /dev/null
@@ -1,280 +0,0 @@
-/* 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. */
-
-#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 -------------------------------- */
-