95efc27edf24bba8d0c7e53d2ef4aead59982826
braney
  Mon Jun 15 18:29:39 2020 -0700
Merging in our gencode merge code to master branch

diff --git src/hg/lib/gencodeToPdb.c src/hg/lib/gencodeToPdb.c
new file mode 100644
index 0000000..8f564ef
--- /dev/null
+++ src/hg/lib/gencodeToPdb.c
@@ -0,0 +1,126 @@
+/* gencodeToPdb.c was originally generated by the autoSql program, which also 
+ * generated gencodeToPdb.h and gencodeToPdb.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "gencodeToPdb.h"
+
+
+
+char *gencodeToPdbCommaSepFieldNames = "transcriptId,pdbId";
+
+void gencodeToPdbStaticLoad(char **row, struct gencodeToPdb *ret)
+/* Load a row from gencodeToPdb table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->transcriptId = row[0];
+ret->pdbId = row[1];
+}
+
+struct gencodeToPdb *gencodeToPdbLoad(char **row)
+/* Load a gencodeToPdb from row fetched with select * from gencodeToPdb
+ * from database.  Dispose of this with gencodeToPdbFree(). */
+{
+struct gencodeToPdb *ret;
+
+AllocVar(ret);
+ret->transcriptId = cloneString(row[0]);
+ret->pdbId = cloneString(row[1]);
+return ret;
+}
+
+struct gencodeToPdb *gencodeToPdbLoadAll(char *fileName) 
+/* Load all gencodeToPdb from a whitespace-separated file.
+ * Dispose of this with gencodeToPdbFreeList(). */
+{
+struct gencodeToPdb *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+
+while (lineFileRow(lf, row))
+    {
+    el = gencodeToPdbLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeToPdb *gencodeToPdbLoadAllByChar(char *fileName, char chopper) 
+/* Load all gencodeToPdb from a chopper separated file.
+ * Dispose of this with gencodeToPdbFreeList(). */
+{
+struct gencodeToPdb *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gencodeToPdbLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeToPdb *gencodeToPdbCommaIn(char **pS, struct gencodeToPdb *ret)
+/* Create a gencodeToPdb out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gencodeToPdb */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->transcriptId = sqlStringComma(&s);
+ret->pdbId = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void gencodeToPdbFree(struct gencodeToPdb **pEl)
+/* Free a single dynamically allocated gencodeToPdb such as created
+ * with gencodeToPdbLoad(). */
+{
+struct gencodeToPdb *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->transcriptId);
+freeMem(el->pdbId);
+freez(pEl);
+}
+
+void gencodeToPdbFreeList(struct gencodeToPdb **pList)
+/* Free a list of dynamically allocated gencodeToPdb's */
+{
+struct gencodeToPdb *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gencodeToPdbFree(&el);
+    }
+*pList = NULL;
+}
+
+void gencodeToPdbOutput(struct gencodeToPdb *el, FILE *f, char sep, char lastSep) 
+/* Print out gencodeToPdb.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->pdbId);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+