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

diff --git src/hg/lib/gencodeAttrs.c src/hg/lib/gencodeAttrs.c
new file mode 100644
index 0000000..151e687
--- /dev/null
+++ src/hg/lib/gencodeAttrs.c
@@ -0,0 +1,187 @@
+/* gencodeAttrs.c was originally generated by the autoSql program, which also 
+ * generated gencodeAttrs.h and gencodeAttrs.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 "gencodeAttrs.h"
+
+
+
+char *gencodeAttrsCommaSepFieldNames = "geneId,geneName,geneType,transcriptId,transcriptName,transcriptType,ccdsId,level,proteinId,transcriptClass";
+
+void gencodeAttrsStaticLoad(char **row, struct gencodeAttrs *ret)
+/* Load a row from gencodeAttrs table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->geneId = row[0];
+ret->geneName = row[1];
+ret->geneType = row[2];
+ret->transcriptId = row[3];
+ret->transcriptName = row[4];
+ret->transcriptType = row[5];
+ret->ccdsId = row[6];
+ret->level = sqlSigned(row[7]);
+ret->proteinId = row[8];
+ret->transcriptClass = row[9];
+}
+
+struct gencodeAttrs *gencodeAttrsLoad(char **row)
+/* Load a gencodeAttrs from row fetched with select * from gencodeAttrs
+ * from database.  Dispose of this with gencodeAttrsFree(). */
+{
+struct gencodeAttrs *ret;
+
+AllocVar(ret);
+ret->geneId = cloneString(row[0]);
+ret->geneName = cloneString(row[1]);
+ret->geneType = cloneString(row[2]);
+ret->transcriptId = cloneString(row[3]);
+ret->transcriptName = cloneString(row[4]);
+ret->transcriptType = cloneString(row[5]);
+ret->ccdsId = cloneString(row[6]);
+ret->level = sqlSigned(row[7]);
+ret->proteinId = cloneString(row[8]);
+ret->transcriptClass = cloneString(row[9]);
+return ret;
+}
+
+struct gencodeAttrs *gencodeAttrsLoadAll(char *fileName) 
+/* Load all gencodeAttrs from a whitespace-separated file.
+ * Dispose of this with gencodeAttrsFreeList(). */
+{
+struct gencodeAttrs *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[10];
+
+while (lineFileRow(lf, row))
+    {
+    el = gencodeAttrsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeAttrs *gencodeAttrsLoadAllByChar(char *fileName, char chopper) 
+/* Load all gencodeAttrs from a chopper separated file.
+ * Dispose of this with gencodeAttrsFreeList(). */
+{
+struct gencodeAttrs *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[10];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = gencodeAttrsLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct gencodeAttrs *gencodeAttrsCommaIn(char **pS, struct gencodeAttrs *ret)
+/* Create a gencodeAttrs out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gencodeAttrs */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->geneId = sqlStringComma(&s);
+ret->geneName = sqlStringComma(&s);
+ret->geneType = sqlStringComma(&s);
+ret->transcriptId = sqlStringComma(&s);
+ret->transcriptName = sqlStringComma(&s);
+ret->transcriptType = sqlStringComma(&s);
+ret->ccdsId = sqlStringComma(&s);
+ret->level = sqlSignedComma(&s);
+ret->proteinId = sqlStringComma(&s);
+ret->transcriptClass = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void gencodeAttrsFree(struct gencodeAttrs **pEl)
+/* Free a single dynamically allocated gencodeAttrs such as created
+ * with gencodeAttrsLoad(). */
+{
+struct gencodeAttrs *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->geneId);
+freeMem(el->geneName);
+freeMem(el->geneType);
+freeMem(el->transcriptId);
+freeMem(el->transcriptName);
+freeMem(el->transcriptType);
+freeMem(el->ccdsId);
+freeMem(el->proteinId);
+freeMem(el->transcriptClass);
+freez(pEl);
+}
+
+void gencodeAttrsFreeList(struct gencodeAttrs **pList)
+/* Free a list of dynamically allocated gencodeAttrs's */
+{
+struct gencodeAttrs *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    gencodeAttrsFree(&el);
+    }
+*pList = NULL;
+}
+
+void gencodeAttrsOutput(struct gencodeAttrs *el, FILE *f, char sep, char lastSep) 
+/* Print out gencodeAttrs.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->geneType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptName);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->ccdsId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->level);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->proteinId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->transcriptClass);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+