15d0836b4dba65919e83ce5ef0aaafe5a0edc72f
angie
  Wed Apr 17 12:49:53 2013 -0700
Making annoGratorGpVar able to handle VCF input too.  In order for a grator tosee what type of input is coming from the primary source, the streamer should
be passed in along with the primary row, as it is for formatters now.
refs #6152

diff --git src/inc/annoGrator.h src/inc/annoGrator.h
index d8b66cf..30058a6 100644
--- src/inc/annoGrator.h
+++ src/inc/annoGrator.h
@@ -1,72 +1,72 @@
 /* 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"
 
 enum annoGratorOverlap
 /* How integrate() method handles overlap (or non-overlap) of internal rows with primary row */
     {
     agoNoConstraint,	// Default: overlap with primary row doesn't matter
     agoMustOverlap,	// integrate() sets RJFilterFail if no internal rows overlap primary
     agoMustNotOverlap   // integrate() sets RJFilterFail if any internal rows overlap primary
     };
 
 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,
+    struct annoRow *(*integrate)(struct annoGrator *self, struct annoStreamRows *primaryData,
 				 boolean *retRJFilterFailed, struct lm *callerLm);
     /* Integrate internal source's data with single row of primary source's data */
 
     void (*setOverlapRule)(struct annoGrator *self, enum annoGratorOverlap rule);
     /* Tell annoGrator how to handle overlap of its rows with primary row. */
 
     // 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
     struct lm *qLm;			// localmem for FIFO queue
     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
     boolean haveRJIncludeFilter;	// TRUE if some filter has !isExclude && rightJoin
     enum annoGratorOverlap overlapRule;	// constraint (if any) on overlap of internal & primary
     };
 
 #endif//ndef ANNOGRATOR_H
 
 // ---------------------- annoGrator default methods -----------------------
 
-struct annoRow *annoGratorIntegrate(struct annoGrator *self, struct annoRow *primaryRow,
+struct annoRow *annoGratorIntegrate(struct annoGrator *self, struct annoStreamRows *primaryData,
 				    boolean *retRJFilterFailed, struct lm *callerLm);
 /* Given a single row from the primary source, get all overlapping rows from internal
  * source, and produce joined output rows.  Use callerLm to allocate the output rows.
  * If retRJFilterFailed is non-NULL:
  * - any overlapping row has a rightJoin filter failure (see annoFilter.h), or
  * - overlap rule is agoMustOverlap and no rows overlap, or
  * - overlap rule is agoMustNotOverlap and any overlapping row is found,
  * then set retRJFilterFailed and stop. */
 
 void annoGratorInit(struct annoGrator *self, struct annoStreamer *mySource);
 /* Initialize an integrator of columns from mySource with (positions of)
  * rows passed to integrate().
  * mySource becomes property of the annoGrator. */
 
 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 annoGratorClose(struct annoStreamer **pSelf);
 /* Free self (including mySource). */