18d303bb4f14e1edff401c8a85276ff1344f0f37
angie
  Tue Apr 3 10:18:14 2012 -0700
Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row
declaring its type and annoRow{Free,Clone} taking a numCols argument
that is meaningless for wig, now annoRow{Free,Clone} take the row's
source annoStreamer as an argument.  The annoStreamer now has public
members (rowType and numCols) that provide all information needed about
the row.  annoStreamer constructors need to set rowType.

diff --git src/lib/annoFormatTab.c src/lib/annoFormatTab.c
index 5ab4fa1..ea0456d 100644
--- src/lib/annoFormatTab.c
+++ src/lib/annoFormatTab.c
@@ -109,94 +109,96 @@
 static char **wordsFromWigRowVals(struct annoRow *row)
 /* Return an array of strings with a single string containing comma-sep per-base wiggle values. */
 {
 float *vector = row->data;
 int len = row->end - row->start;
 struct dyString *dy = dyStringNew(10*len);
 int i;
 for (i = 0;  i < len;  i++)
     dyStringPrintf(dy, "%f,", vector[i]);
 char **words;
 AllocArray(words, 1);
 words[0] = dyStringCannibalize(&dy);
 return words;
 }
 
-static char **wordsFromRow(struct annoRow *row, boolean *retFreeWhenDone)
-/* If row->type is arWords, return its words.  Otherwise translate row->data into words. */
+static char **wordsFromRow(struct annoRow *row, struct annoStreamer *source,
+			   boolean *retFreeWhenDone)
+/* If source->rowType is arWords, return its words.  Otherwise translate row->data into words. */
 {
 if (row == NULL)
     return NULL;
 boolean freeWhenDone = FALSE;
 char **words = NULL;
-if (row->type == arWords)
+if (source->rowType == arWords || source->rowType == arVcf)
     words = row->data;
-else if (row->type == arWig)
+else if (source->rowType == arWig)
     {
     freeWhenDone = TRUE;
     //#*** config options: avg? more stats? list of values?
     boolean doAvg = FALSE;
     if (doAvg)
 	words = wordsFromWigRowAvg(row);
     else
 	words = wordsFromWigRowVals(row);
     }
 else
-    errAbort("annoFormatTab: unrecognized row type %d", row->type);
+    errAbort("annoFormatTab: unrecognized row type %d", source->rowType);
 if (retFreeWhenDone != NULL)
     *retFreeWhenDone = freeWhenDone;
 return words;
 }
 
 INLINE void freeWords1(char **words)
 /* Free words and words[0] (alloc'd by wordsFromWig* above. */
 {
 freeMem(words[0]);
 freeMem(words);
 }
 
 static void aftFormatOne(struct annoFormatter *vSelf)
 /* Print out tab-separated columns that we have gathered in prior calls to aftCollect,
  * and start over fresh for the next line of output. */
 {
 struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
 slReverse(&(self->gratorRowLists));
 // How many rows did each grator give us, and what's the largest # of rows?
 int maxRows = 1;
 int i;
 struct slRef *grRef;
 int numGrators = slCount(self->gratorRowLists);
 for (i = 0, grRef = self->gratorRowLists;  i < numGrators;  i++, grRef = grRef->next)
     {
     int gratorRowCount = slCount(grRef->val);
     if (gratorRowCount > maxRows)
 	maxRows = gratorRowCount;
     }
 // Print out enough rows to make sure that all grator rows are included.
+struct annoStreamer *primarySource = vSelf->query->primarySource;
 for (i = 0;  i < maxRows;  i++)
     {
     boolean freeWhenDone = FALSE;
-    char **primaryData = wordsFromRow(self->primaryRow, &freeWhenDone);
-    printColumns(self->f, vSelf->query->primarySource, primaryData, TRUE);
+    char **primaryData = wordsFromRow(self->primaryRow, primarySource, &freeWhenDone);
+    printColumns(self->f, primarySource, primaryData, TRUE);
     if (freeWhenDone)
 	freeWords1(primaryData);
     struct annoStreamer *grator = (struct annoStreamer *)self->formatter.query->integrators;
     for (grRef = self->gratorRowLists;  grRef != NULL;  grRef = grRef->next,
 	     grator = grator->next)
 	{
 	struct annoRow *gratorRow = slElementFromIx(grRef->val, i);
-	char **gratorWords = wordsFromRow(gratorRow, &freeWhenDone);
+	char **gratorWords = wordsFromRow(gratorRow, grator, &freeWhenDone);
 	printColumns(self->f, grator, gratorWords, FALSE);
 	if (freeWhenDone)
 	    freeWords1(gratorWords);
 	}
     fputc('\n', self->f);
     }
 self->primaryRow = NULL;
 slFreeList(&(self->gratorRowLists));
 }
 
 static void aftClose(struct annoFormatter **pVSelf)
 /* Close file handle, free self. */
 {
 if (pVSelf == NULL)
     return;