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/pgSiftPred.c src/hg/lib/pgSiftPred.c
deleted file mode 100644
index ab4f9ae..0000000
--- src/hg/lib/pgSiftPred.c
+++ /dev/null
@@ -1,261 +0,0 @@
-/* pgSiftPred.c was originally generated by the autoSql program, which also 
- * generated pgSiftPred.h and pgSiftPred.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 "hdb.h"
-#include "pgSiftPred.h"
-
-
-void pgSiftPredStaticLoadWithNull(char **row, struct pgSiftPred *ret)
-/* Load a row from pgSiftPred table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->chrom = row[0];
-if (row[1] != NULL)
-    {
-    ret->chromStart = needMem(sizeof(*(ret->chromStart)));
-    *(ret->chromStart) = sqlUnsigned(row[1]);
-    }
-else
-    {
-    ret->chromStart = NULL;
-    }
-if (row[2] != NULL)
-    {
-    ret->chromEnd = needMem(sizeof(*(ret->chromEnd)));
-    *(ret->chromEnd) = sqlUnsigned(row[2]);
-    }
-else
-    {
-    ret->chromEnd = NULL;
-    }
-ret->prediction = row[3];
-ret->geneId = row[4];
-ret->geneName = row[5];
-ret->geneDesc = row[6];
-ret->protFamDesc = row[7];
-ret->omimDisease = row[8];
-ret->aveAlleleFreq = row[9];
-ret->ceuAlleleFreq = row[10];
-}
-
-struct pgSiftPred *pgSiftPredLoadWithNull(char **row)
-/* Load a pgSiftPred from row fetched with select * from pgSiftPred
- * from database.  Dispose of this with pgSiftPredFree(). */
-{
-struct pgSiftPred *ret;
-
-AllocVar(ret);
-ret->chrom = cloneString(row[0]);
-if (row[1] != NULL)
-    {
-    ret->chromStart = needMem(sizeof(*(ret->chromStart)));
-    *(ret->chromStart) = sqlUnsigned(row[1]);
-    }
-else
-    {
-    ret->chromStart = NULL;
-    }
-if (row[2] != NULL)
-    {
-    ret->chromEnd = needMem(sizeof(*(ret->chromEnd)));
-    *(ret->chromEnd) = sqlUnsigned(row[2]);
-    }
-else
-    {
-    ret->chromEnd = NULL;
-    }
-ret->prediction = cloneString(row[3]);
-ret->geneId = cloneString(row[4]);
-ret->geneName = cloneString(row[5]);
-ret->geneDesc = cloneString(row[6]);
-ret->protFamDesc = cloneString(row[7]);
-ret->omimDisease = cloneString(row[8]);
-ret->aveAlleleFreq = cloneString(row[9]);
-ret->ceuAlleleFreq = cloneString(row[10]);
-return ret;
-}
-
-struct pgSiftPred *pgSiftPredLoadAll(char *fileName) 
-/* Load all pgSiftPred from a whitespace-separated file.
- * Dispose of this with pgSiftPredFreeList(). */
-{
-struct pgSiftPred *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[11];
-
-while (lineFileRow(lf, row))
-    {
-    el = pgSiftPredLoadWithNull(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct pgSiftPred *pgSiftPredLoadAllByChar(char *fileName, char chopper) 
-/* Load all pgSiftPred from a chopper separated file.
- * Dispose of this with pgSiftPredFreeList(). */
-{
-struct pgSiftPred *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[11];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = pgSiftPredLoadWithNull(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct pgSiftPred *pgSiftPredCommaIn(char **pS, struct pgSiftPred *ret)
-/* Create a pgSiftPred out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new pgSiftPred */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->chrom = sqlStringComma(&s);
-ret->chromStart = needMem(sizeof(unsigned));
-*(ret->chromStart) = sqlUnsignedComma(&s);
-ret->chromEnd = needMem(sizeof(unsigned));
-*(ret->chromEnd) = sqlUnsignedComma(&s);
-ret->prediction = sqlStringComma(&s);
-ret->geneId = sqlStringComma(&s);
-ret->geneName = sqlStringComma(&s);
-ret->geneDesc = sqlStringComma(&s);
-ret->protFamDesc = sqlStringComma(&s);
-ret->omimDisease = sqlStringComma(&s);
-ret->aveAlleleFreq = sqlStringComma(&s);
-ret->ceuAlleleFreq = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void pgSiftPredFree(struct pgSiftPred **pEl)
-/* Free a single dynamically allocated pgSiftPred such as created
- * with pgSiftPredLoad(). */
-{
-struct pgSiftPred *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->prediction);
-freeMem(el->geneId);
-freeMem(el->geneName);
-freeMem(el->geneDesc);
-freeMem(el->protFamDesc);
-freeMem(el->omimDisease);
-freeMem(el->aveAlleleFreq);
-freeMem(el->ceuAlleleFreq);
-freez(pEl);
-}
-
-void pgSiftPredFreeList(struct pgSiftPred **pList)
-/* Free a list of dynamically allocated pgSiftPred's */
-{
-struct pgSiftPred *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    pgSiftPredFree(&el);
-    }
-*pList = NULL;
-}
-
-void pgSiftPredOutput(struct pgSiftPred *el, FILE *f, char sep, char lastSep) 
-/* Print out pgSiftPred.  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->prediction);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneId);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->geneDesc);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->protFamDesc);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->omimDisease);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->aveAlleleFreq);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->ceuAlleleFreq);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-
-void printPgSiftPred (char *db, char *tableName, struct pgSnp *item)
-/* print the predictions for an hgc item click for a pgSnp track */
-{
-struct pgSiftPred *el;
-struct sqlResult *sr;
-char **row;
-char query[512];
-struct sqlConnection *conn = hAllocConn(db);
-
-sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart = %d and chromEnd = %d",
-    tableName, item->chrom, item->chromStart, item->chromEnd);
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    el = pgSiftPredLoadWithNull(row);
-    printf("<br><b>SIFT prediction</b>: %s\n", el->prediction);
-    printf("<ul>");
-    if (el->geneId != NULL && differentString(el->geneId, ""))
-        printf("<li>Gene ID: %s</li>\n", el->geneId);
-    if (el->geneName != NULL && differentString(el->geneName, ""))
-        printf("<li>Gene name: %s</li>\n", el->geneName);
-    if (el->geneDesc != NULL && differentString(el->geneDesc, ""))
-        printf("<li>Gene description: %s</li>\n", el->geneDesc);
-    if (el->protFamDesc != NULL && differentString(el->protFamDesc, ""))
-        printf("<li>Protein family description: %s</li>\n", el->protFamDesc);
-    if (el->omimDisease != NULL && differentString(el->omimDisease, ""))
-        printf("<li>OMIM disease: %s</li>\n", el->omimDisease);
-    if (el->aveAlleleFreq != NULL && differentString(el->aveAlleleFreq, ""))
-        printf("<li>Average allele frequency: %s</li>\n", el->aveAlleleFreq);
-    if (el->ceuAlleleFreq != NULL && differentString(el->ceuAlleleFreq, ""))
-	printf("<li>CEU allele frequency: %s</li>\n", el->ceuAlleleFreq);
-    printf("</ul>\n");
-    }
-}