05316c62e54dfd3cac589a1ae6001e84c357959b
angie
  Mon Apr 23 08:24:28 2012 -0700
Feature #6152 (Variant Annotation Tool): enhancement to filter logic:filters can be for inclusion or exclusion when the condition is met,
based on the new filter->isExclude.  When a filter is set to rightJoin
and it is for inclusion, annoGratorIntegrate propagates rightJoin
failure if no rows overlap since the condition for inclusion has not
been met.

diff --git src/inc/annoGrator.h src/inc/annoGrator.h
index 64b0c24..5bc625a 100644
--- src/inc/annoGrator.h
+++ src/inc/annoGrator.h
@@ -1,53 +1,55 @@
 /* annoGrator -- annoStreamer that integrates genomic annotations from two annoStreamers */
 
 // Subclasses of annoGrator can add new columns of output such as predicted 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:
     struct annoRow *(*integrate)(struct annoGrator *self, struct annoRow *primaryRow,
 				 boolean *retRJFilterFailed);
     /* Integrate internal source's data with single row of primary source's data */
 
     // Private members -- callers are on the honor system to access these using only methods above.
     struct annoStreamer *mySource;	// internal source
+    struct annoRow *qHead;		// head of FIFO queue of rows from internal source
+    struct annoRow *qTail;		// head of FIFO queue of rows from internal source
     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
+    boolean haveRJIncludeFilter;	// TRUE if some filter has !isExclude && rightJoin;
+					// if TRUE and there are no overlapping rows, then RJ fail
     };
 
 #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). */