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/cgilib/bgiSnp.c src/hg/cgilib/bgiSnp.c
new file mode 100644
index 0000000..8800b63
--- /dev/null
+++ src/hg/cgilib/bgiSnp.c
@@ -0,0 +1,236 @@
+/* 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 -------------------------------- */
+