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/bgiSnp.c src/hg/lib/bgiSnp.c
deleted file mode 100644
index 8800b63..0000000
--- src/hg/lib/bgiSnp.c
+++ /dev/null
@@ -1,236 +0,0 @@
-/* bgiSnp.c was originally generated by the autoSql program, which also 
- * generated bgiSnp.h and bgiSnp.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 "bgiSnp.h"
-
-
-void bgiSnpStaticLoad(char **row, struct bgiSnp *ret)
-/* Load a row from bgiSnp 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];
-strcpy(ret->snpType, row[4]);
-ret->readStart = sqlUnsigned(row[5]);
-ret->readEnd = sqlUnsigned(row[6]);
-ret->qualChr = sqlUnsigned(row[7]);
-ret->qualReads = sqlUnsigned(row[8]);
-ret->snpSeq = row[9];
-ret->readName = row[10];
-strcpy(ret->readDir, row[11]);
-strcpy(ret->inBroiler, row[12]);
-strcpy(ret->inLayer, row[13]);
-strcpy(ret->inSilkie, row[14]);
-ret->primerL = row[15];
-ret->primerR = row[16];
-strcpy(ret->questionM, row[17]);
-ret->extra = row[18];
-}
-
-struct bgiSnp *bgiSnpLoad(char **row)
-/* Load a bgiSnp from row fetched with select * from bgiSnp
- * from database.  Dispose of this with bgiSnpFree(). */
-{
-struct bgiSnp *ret;
-AllocVar(ret);
-ret->chrom = cloneString(row[0]);
-ret->chromStart = sqlUnsigned(row[1]);
-ret->chromEnd = sqlUnsigned(row[2]);
-ret->name = cloneString(row[3]);
-strcpy(ret->snpType, row[4]);
-ret->readStart = sqlUnsigned(row[5]);
-ret->readEnd = sqlUnsigned(row[6]);
-ret->qualChr = sqlUnsigned(row[7]);
-ret->qualReads = sqlUnsigned(row[8]);
-ret->snpSeq = cloneString(row[9]);
-ret->readName = cloneString(row[10]);
-strcpy(ret->readDir, row[11]);
-strcpy(ret->inBroiler, row[12]);
-strcpy(ret->inLayer, row[13]);
-strcpy(ret->inSilkie, row[14]);
-ret->primerL = cloneString(row[15]);
-ret->primerR = cloneString(row[16]);
-strcpy(ret->questionM, row[17]);
-ret->extra = cloneString(row[18]);
-return ret;
-}
-
-struct bgiSnp *bgiSnpLoadAll(char *fileName) 
-/* Load all bgiSnp from a whitespace-separated file.
- * Dispose of this with bgiSnpFreeList(). */
-{
-struct bgiSnp *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[19];
-
-while (lineFileRow(lf, row))
-    {
-    el = bgiSnpLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct bgiSnp *bgiSnpLoadAllByChar(char *fileName, char chopper) 
-/* Load all bgiSnp from a chopper separated file.
- * Dispose of this with bgiSnpFreeList(). */
-{
-struct bgiSnp *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[19];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = bgiSnpLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct bgiSnp *bgiSnpCommaIn(char **pS, struct bgiSnp *ret)
-/* Create a bgiSnp out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new bgiSnp */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->chrom = sqlStringComma(&s);
-ret->chromStart = sqlUnsignedComma(&s);
-ret->chromEnd = sqlUnsignedComma(&s);
-ret->name = sqlStringComma(&s);
-sqlFixedStringComma(&s, ret->snpType, sizeof(ret->snpType));
-ret->readStart = sqlUnsignedComma(&s);
-ret->readEnd = sqlUnsignedComma(&s);
-ret->qualChr = sqlUnsignedComma(&s);
-ret->qualReads = sqlUnsignedComma(&s);
-ret->snpSeq = sqlStringComma(&s);
-ret->readName = sqlStringComma(&s);
-sqlFixedStringComma(&s, ret->readDir, sizeof(ret->readDir));
-sqlFixedStringComma(&s, ret->inBroiler, sizeof(ret->inBroiler));
-sqlFixedStringComma(&s, ret->inLayer, sizeof(ret->inLayer));
-sqlFixedStringComma(&s, ret->inSilkie, sizeof(ret->inSilkie));
-ret->primerL = sqlStringComma(&s);
-ret->primerR = sqlStringComma(&s);
-sqlFixedStringComma(&s, ret->questionM, sizeof(ret->questionM));
-ret->extra = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void bgiSnpFree(struct bgiSnp **pEl)
-/* Free a single dynamically allocated bgiSnp such as created
- * with bgiSnpLoad(). */
-{
-struct bgiSnp *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->snpSeq);
-freeMem(el->readName);
-freeMem(el->primerL);
-freeMem(el->primerR);
-freeMem(el->extra);
-freez(pEl);
-}
-
-void bgiSnpFreeList(struct bgiSnp **pList)
-/* Free a list of dynamically allocated bgiSnp's */
-{
-struct bgiSnp *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    bgiSnpFree(&el);
-    }
-*pList = NULL;
-}
-
-void bgiSnpOutput(struct bgiSnp *el, FILE *f, char sep, char lastSep) 
-/* Print out bgiSnp.  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);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->snpType);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->readStart);
-fputc(sep,f);
-fprintf(f, "%u", el->readEnd);
-fputc(sep,f);
-fprintf(f, "%u", el->qualChr);
-fputc(sep,f);
-fprintf(f, "%u", el->qualReads);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->snpSeq);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->readName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->readDir);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->inBroiler);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->inLayer);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->inSilkie);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->primerL);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->primerR);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->questionM);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->extra);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-