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

diff --git src/hg/lib/gencodeExonSupport.c src/hg/lib/gencodeExonSupport.c
new file mode 100644
index 0000000..96d383f
--- /dev/null
+++ src/hg/lib/gencodeExonSupport.c
@@ -0,0 +1,160 @@
+/* gencodeExonSupport.c was originally generated by the autoSql program, which also 
+ * generated gencodeExonSupport.h and gencodeExonSupport.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 "gencodeExonSupport.h"
+
+
+
+char *gencodeExonSupportCommaSepFieldNames = "transcriptId,seqId,seqSrc,exonId,chrom,chromStart,chromEnd";
+
+void gencodeExonSupportStaticLoad(char **row, struct gencodeExonSupport *ret)
+/* Load a row from gencodeExonSupport table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->transcriptId = row[0];
+ret->seqId = row[1];
+ret->seqSrc = row[2];
+ret->exonId = row[3];
+ret->chrom = row[4];
+ret->chromStart = sqlUnsigned(row[5]);
+ret->chromEnd = sqlUnsigned(row[6]);
+}
+
+struct gencodeExonSupport *gencodeExonSupportLoad(char **row)
+/* Load a gencodeExonSupport from row fetched with select * from gencodeExonSupport
+ * from database.  Dispose of this with gencodeExonSupportFree(). */
+{
+struct gencodeExonSupport *ret;
+
+AllocVar(ret);
+ret->transcriptId = cloneString(row[0]);
+ret->seqId = cloneString(row[1]);
+ret->seqSrc = cloneString(row[2]);
+ret->exonId = cloneString(row[3]);
+ret->chrom = cloneString(row[4]);
+ret->chromStart = sqlUnsigned(row[5]);
+ret->chromEnd = sqlUnsigned(row[6]);
+return ret;
+}
+
+struct gencodeExonSupport *gencodeExonSupportLoadAll(char *fileName) 
+/* Load all gencodeExonSupport from a whitespace-separated file.
+ * Dispose of this with gencodeExonSupportFreeList(). */
+{
+struct gencodeExonSupport *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileRow(lf, row))
+    {
+    el = gencodeExonSupportLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeExonSupport *gencodeExonSupportLoadAllByChar(char *fileName, char chopper) 
+/* Load all gencodeExonSupport from a chopper separated file.
+ * Dispose of this with gencodeExonSupportFreeList(). */
+{
+struct gencodeExonSupport *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gencodeExonSupportLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeExonSupport *gencodeExonSupportCommaIn(char **pS, struct gencodeExonSupport *ret)
+/* Create a gencodeExonSupport out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gencodeExonSupport */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->transcriptId = sqlStringComma(&s);
+ret->seqId = sqlStringComma(&s);
+ret->seqSrc = sqlStringComma(&s);
+ret->exonId = sqlStringComma(&s);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void gencodeExonSupportFree(struct gencodeExonSupport **pEl)
+/* Free a single dynamically allocated gencodeExonSupport such as created
+ * with gencodeExonSupportLoad(). */
+{
+struct gencodeExonSupport *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->transcriptId);
+freeMem(el->seqId);
+freeMem(el->seqSrc);
+freeMem(el->exonId);
+freeMem(el->chrom);
+freez(pEl);
+}
+
+void gencodeExonSupportFreeList(struct gencodeExonSupport **pList)
+/* Free a list of dynamically allocated gencodeExonSupport's */
+{
+struct gencodeExonSupport *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gencodeExonSupportFree(&el);
+    }
+*pList = NULL;
+}
+
+void gencodeExonSupportOutput(struct gencodeExonSupport *el, FILE *f, char sep, char lastSep) 
+/* Print out gencodeExonSupport.  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->seqId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->seqSrc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->exonId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+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(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+