be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/lib/fieldedTable.c src/lib/fieldedTable.c
index 0742669..79a4658 100644
--- src/lib/fieldedTable.c
+++ src/lib/fieldedTable.c
@@ -178,86 +178,96 @@
 if (doReverse)
     slReverse(&pairList);
 
 /* Convert rowList to have same order. */
 struct fieldedRow *newList = NULL;
 for (pair = pairList; pair != NULL; pair = pair->next)
     {
     fr = pair->val;
     slAddHead(&newList, fr);
     }
 slReverse(&newList);
 table->rowList = newList;
 lmCleanup(&lm);
 }
 
-struct fieldedTable *fieldedTableFromTabFile(char *fileName, char *reportFileName, 
+struct fieldedTable *fieldedTableReadTabHeader(struct lineFile *lf, 
     char *requiredFields[], int requiredCount)
-/* Read table from tab-separated file with a #header line that defines the fields.  Ensures
- * all requiredFields (if any) are present.  The reportFileName is just used for error reporting and 
- * should be NULL for most purposes.  This is used by edwSubmit though which
- * first copies to a local file, and we want to report errors from the remote file. 
- * We do know the remote file exists at least, because we just copied it. */
-{
-/* Open file with fileName */
-struct lineFile *lf = netLineFileOpen(fileName);
-
-/* Substitute in reportFileName for error reporting */
-if (reportFileName != NULL)
-    {
-    if (differentString(reportFileName, fileName))
-        {
-	freeMem(lf->fileName);
-	lf->fileName = cloneString(reportFileName);
-	}
-    }
-else
+/* Read in first line of file treating it as a fieldedTable header line. 
+ * Used in combination with fieldedTableReadNextRow() */
 {
-    reportFileName = fileName;
-    }
-
 /* Get first line and turn it into field list. */
 char *line;
 if (!lineFileNext(lf, &line, NULL))
-   errAbort("%s is empty", reportFileName);
+   errAbort("%s is empty", lf->fileName);
 boolean startsSharp = FALSE;
 if (line[0] == '#')
    {
    line = skipLeadingSpaces(line+1);
    startsSharp = TRUE;
    }
    
 int fieldCount = chopByChar(line, '\t', NULL, 0);
 char *fields[fieldCount];
 chopTabs(line, fields);
 
 /* Make sure that all required fields are present. */
 int i;
 for (i = 0; i < requiredCount; ++i)
     {
     char *required = requiredFields[i];
     int ix = stringArrayIx(required, fields, fieldCount);
     if (ix < 0)
-        errAbort("%s is missing required field '%s'", reportFileName, required);
+        errAbort("%s is missing required field '%s'", lf->fileName, required);
     }
 
 /* Create fieldedTable . */
-struct fieldedTable *table = fieldedTableNew(reportFileName, fields, fieldCount);
+struct fieldedTable *table = fieldedTableNew(lf->fileName, fields, fieldCount);
 table->startsSharp = startsSharp;
-while (lineFileRowTab(lf, fields))
+return table;
+}
+
+struct fieldedTable *fieldedTableFromTabFile(char *fileName, char *reportFileName, 
+    char *requiredFields[], int requiredCount)
+/* Read table from tab-separated file with a #header line that defines the fields.  Ensures
+ * all requiredFields (if any) are present.  The reportFileName is just used for error reporting and 
+ * should be NULL for most purposes.  This is used by edwSubmit though which
+ * first copies to a local file, and we want to report errors from the remote file. 
+ * We do know the remote file exists at least, because we just copied it. */
+{
+/* Open file with fileName */
+struct lineFile *lf = netLineFileOpen(fileName);
+
+/* Substitute in reportFileName for error reporting */
+if (reportFileName != NULL)
+    {
+    if (differentString(reportFileName, fileName))
+        {
+	freeMem(lf->fileName);
+	lf->fileName = cloneString(reportFileName);
+	}
+    }
+else
+    {
+    reportFileName = fileName;
+    }
+
+struct fieldedTable *table = fieldedTableReadTabHeader(lf, requiredFields, requiredCount);
+char *row[table->fieldCount];
+while (lineFileNextRowTab(lf, row, table->fieldCount))
     {
-    fieldedTableAdd(table, fields, fieldCount, lf->lineIx);
+    fieldedTableAdd(table, row, table->fieldCount, lf->lineIx);
     }
 
 /* Clean up and go home. */
 lineFileClose(&lf);
 return table;
 }
 
 void fieldedTableToTabFileWithId(struct fieldedTable *table, char *fileName, 
     char *idField, int startId)
 /* Write out a fielded table back to file.  If idField is non-NULL it will be added
  * to the start of each output line as a steadily incrementing integer starting with startId. */
 {
 FILE *f = mustOpen(fileName, "w");
 
 /* Write out header row with optional leading # */