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/inc/annoGrator.h src/inc/annoGrator.h
index 259d525..fd173f8 100644
--- src/inc/annoGrator.h
+++ src/inc/annoGrator.h
@@ -1,52 +1,51 @@
 /* annoGrator -- annoStreamer that integrates genomic annotations from two annoStreamers */
 
 // Subclasses of annoGrator can do value-add things such as predict function given
 // a variant and a gene; the base class simply intersects by position, returning
 // all rows from its internal data source that overlap the position of primaryRow.
 // The interface to an annoGrator is almost the same as the interface to an annoStreamer,
 // *except* you call integrate() instead of nextRow().
 
 #ifndef ANNOGRATOR_H
 #define ANNOGRATOR_H
 
 #include "annoStreamer.h"
 
 struct annoGrator
 /* annoStreamer that can integrate an internal annoStreamer's data
  * with data from a primary source. */
     {
     struct annoStreamer streamer;	// external annoStreamer interface
     // Public method that makes this a 'grator:
     // Integrate own source's data with single row of primary source's data
     struct annoRow *(*integrate)(struct annoGrator *self, struct annoRow *primaryRow,
 				 boolean *retRJFilterFailed);
     // Private members -- callers are on the honor system to access these using only methods above.
     struct annoStreamer *mySource;	// internal source
-    int numSrcCols;			// cache the number of columns we get from mySource
     char *prevPChrom;			// for detection of unsorted input from primary
     uint prevPStart;			// for detection of unsorted input from primary
     boolean eof;			// stop asking internal source for rows when it's done
     struct annoRow *qHead;		// head of FIFO queue of rows from internal source
     struct annoRow *qTail;		// head of FIFO queue of rows from internal source
     };
 
 #endif//ndef ANNOGRATOR_H
 
 // ---------------------- annoGrator default methods -----------------------
 
 struct annoRow *annoGratorIntegrate(struct annoGrator *self, struct annoRow *primaryRow,
 				    boolean *retRJFilterFailed);
 /* Given a single row from the primary source, get all overlapping rows from internal
  * source, and produce joined output rows.  If retRJFilterFailed is non-NULL and any
  * overlapping row has a rightJoin filter failure (see annoFilter.h),
  * set retRJFilterFailed and stop. */
 
 struct annoGrator *annoGratorNew(struct annoStreamer *mySource);
 /* Make a new integrator of columns from mySource with (positions of) rows passed to integrate().
  * mySource becomes property of the new annoGrator. */
 
 void annoGratorSetQuery(struct annoStreamer *vSelf, struct annoGratorQuery *query);
 /* Set query (to be called only by annoGratorQuery which is created after streamers). */
 
 void annoGratorClose(struct annoStreamer **pSelf);
 /* Free self (including mySource). */