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/chr18deletions.c src/hg/cgilib/chr18deletions.c
new file mode 100644
index 0000000..b6ba86d
--- /dev/null
+++ src/hg/cgilib/chr18deletions.c
@@ -0,0 +1,235 @@
+/* chr18deletions.c was originally generated by the autoSql program, which also 
+ * generated chr18deletions.h and chr18deletions.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 "chr18deletions.h"
+
+
+struct chr18deletions *chr18deletionsLoad(char **row)
+/* Load a chr18deletions from row fetched with select * from chr18deletions
+ * from database.  Dispose of this with chr18deletionsFree(). */
+{
+struct chr18deletions *ret;
+int sizeOne;
+
+AllocVar(ret);
+ret->ssCount = sqlUnsigned(row[6]);
+ret->seCount = sqlUnsigned(row[8]);
+ret->lsCount = sqlUnsigned(row[10]);
+ret->leCount = sqlUnsigned(row[12]);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlSigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+strcpy(ret->strand, row[5]);
+sqlUnsignedDynamicArray(row[7], &ret->smallStarts, &sizeOne);
+assert(sizeOne == ret->ssCount);
+sqlUnsignedDynamicArray(row[9], &ret->smallEnds, &sizeOne);
+assert(sizeOne == ret->seCount);
+sqlUnsignedDynamicArray(row[11], &ret->largeStarts, &sizeOne);
+assert(sizeOne == ret->lsCount);
+sqlUnsignedDynamicArray(row[13], &ret->largeEnds, &sizeOne);
+assert(sizeOne == ret->leCount);
+return ret;
+}
+
+struct chr18deletions *chr18deletionsLoadAll(char *fileName) 
+/* Load all chr18deletions from a tab-separated file.
+ * Dispose of this with chr18deletionsFreeList(). */
+{
+struct chr18deletions *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileRow(lf, row))
+    {
+    el = chr18deletionsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct chr18deletions *chr18deletionsLoadWhere(struct sqlConnection *conn, char *table, char *where)
+/* Load all chr18deletions from table that satisfy where clause. The
+ * where clause may be NULL in which case whole table is loaded
+ * Dispose of this with chr18deletionsFreeList(). */
+{
+struct chr18deletions *list = NULL, *el;
+struct dyString *query = dyStringNew(256);
+struct sqlResult *sr;
+char **row;
+
+sqlDyStringPrintf(query, "select * from %s", table);
+if (where != NULL)
+    dyStringPrintf(query, " where %s", where);
+sr = sqlGetResult(conn, query->string);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = chr18deletionsLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+dyStringFree(&query);
+return list;
+}
+
+struct chr18deletions *chr18deletionsCommaIn(char **pS, struct chr18deletions *ret)
+/* Create a chr18deletions out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new chr18deletions */
+{
+char *s = *pS;
+int i;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlSignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->name = sqlStringComma(&s);
+ret->score = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->ssCount = sqlUnsignedComma(&s);
+s = sqlEatChar(s, '{');
+AllocArray(ret->smallStarts, ret->ssCount);
+for (i=0; i<ret->ssCount; ++i)
+    {
+    ret->smallStarts[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+ret->seCount = sqlUnsignedComma(&s);
+s = sqlEatChar(s, '{');
+AllocArray(ret->smallEnds, ret->seCount);
+for (i=0; i<ret->seCount; ++i)
+    {
+    ret->smallEnds[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+ret->lsCount = sqlUnsignedComma(&s);
+s = sqlEatChar(s, '{');
+AllocArray(ret->largeStarts, ret->lsCount);
+for (i=0; i<ret->lsCount; ++i)
+    {
+    ret->largeStarts[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+ret->leCount = sqlUnsignedComma(&s);
+s = sqlEatChar(s, '{');
+AllocArray(ret->largeEnds, ret->leCount);
+for (i=0; i<ret->leCount; ++i)
+    {
+    ret->largeEnds[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+*pS = s;
+return ret;
+}
+
+void chr18deletionsFree(struct chr18deletions **pEl)
+/* Free a single dynamically allocated chr18deletions such as created
+ * with chr18deletionsLoad(). */
+{
+struct chr18deletions *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->smallStarts);
+freeMem(el->smallEnds);
+freeMem(el->largeStarts);
+freeMem(el->largeEnds);
+freez(pEl);
+}
+
+void chr18deletionsFreeList(struct chr18deletions **pList)
+/* Free a list of dynamically allocated chr18deletions's */
+{
+struct chr18deletions *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    chr18deletionsFree(&el);
+    }
+*pList = NULL;
+}
+
+void chr18deletionsOutput(struct chr18deletions *el, FILE *f, char sep, char lastSep) 
+/* Print out chr18deletions.  Separate fields with sep. Follow last field with lastSep. */
+{
+int i;
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", 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->score);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->ssCount);
+fputc(sep,f);
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->ssCount; ++i)
+    {
+    fprintf(f, "%u", el->smallStarts[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+fputc(sep,f);
+fprintf(f, "%u", el->seCount);
+fputc(sep,f);
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->seCount; ++i)
+    {
+    fprintf(f, "%u", el->smallEnds[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+fputc(sep,f);
+fprintf(f, "%u", el->lsCount);
+fputc(sep,f);
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->lsCount; ++i)
+    {
+    fprintf(f, "%u", el->largeStarts[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+fputc(sep,f);
+fprintf(f, "%u", el->leCount);
+fputc(sep,f);
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->leCount; ++i)
+    {
+    fprintf(f, "%u", el->largeEnds[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+fputc(lastSep,f);
+}
+