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

diff --git src/hg/lib/gencodeToPubMed.c src/hg/lib/gencodeToPubMed.c
new file mode 100644
index 0000000..3faa4d8
--- /dev/null
+++ src/hg/lib/gencodeToPubMed.c
@@ -0,0 +1,123 @@
+/* gencodeToPubMed.c was originally generated by the autoSql program, which also 
+ * generated gencodeToPubMed.h and gencodeToPubMed.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 "gencodeToPubMed.h"
+
+
+
+char *gencodeToPubMedCommaSepFieldNames = "transcriptId,pubMedId";
+
+void gencodeToPubMedStaticLoad(char **row, struct gencodeToPubMed *ret)
+/* Load a row from gencodeToPubMed table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->transcriptId = row[0];
+ret->pubMedId = sqlSigned(row[1]);
+}
+
+struct gencodeToPubMed *gencodeToPubMedLoad(char **row)
+/* Load a gencodeToPubMed from row fetched with select * from gencodeToPubMed
+ * from database.  Dispose of this with gencodeToPubMedFree(). */
+{
+struct gencodeToPubMed *ret;
+
+AllocVar(ret);
+ret->transcriptId = cloneString(row[0]);
+ret->pubMedId = sqlSigned(row[1]);
+return ret;
+}
+
+struct gencodeToPubMed *gencodeToPubMedLoadAll(char *fileName) 
+/* Load all gencodeToPubMed from a whitespace-separated file.
+ * Dispose of this with gencodeToPubMedFreeList(). */
+{
+struct gencodeToPubMed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+
+while (lineFileRow(lf, row))
+    {
+    el = gencodeToPubMedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeToPubMed *gencodeToPubMedLoadAllByChar(char *fileName, char chopper) 
+/* Load all gencodeToPubMed from a chopper separated file.
+ * Dispose of this with gencodeToPubMedFreeList(). */
+{
+struct gencodeToPubMed *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gencodeToPubMedLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeToPubMed *gencodeToPubMedCommaIn(char **pS, struct gencodeToPubMed *ret)
+/* Create a gencodeToPubMed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gencodeToPubMed */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->transcriptId = sqlStringComma(&s);
+ret->pubMedId = sqlSignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void gencodeToPubMedFree(struct gencodeToPubMed **pEl)
+/* Free a single dynamically allocated gencodeToPubMed such as created
+ * with gencodeToPubMedLoad(). */
+{
+struct gencodeToPubMed *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->transcriptId);
+freez(pEl);
+}
+
+void gencodeToPubMedFreeList(struct gencodeToPubMed **pList)
+/* Free a list of dynamically allocated gencodeToPubMed's */
+{
+struct gencodeToPubMed *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gencodeToPubMedFree(&el);
+    }
+*pList = NULL;
+}
+
+void gencodeToPubMedOutput(struct gencodeToPubMed *el, FILE *f, char sep, char lastSep) 
+/* Print out gencodeToPubMed.  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);
+fprintf(f, "%d", el->pubMedId);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+