cf293df150f4b256d195e90b5a20817d8479ece0
galt
  Sat Jul 2 13:17:59 2016 -0700
fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.

diff --git src/inc/genoFind.h src/inc/genoFind.h
index 34ab7f4..39c063a 100644
--- src/inc/genoFind.h
+++ src/inc/genoFind.h
@@ -367,19 +367,19 @@
    int minScore, struct gfOutput *out);
 /* Chop up query into pieces, align each in translated space, and stitch back
  * together again as nucleotides. */
 
 struct gfClump *gfPcrClumps(struct genoFind *gf, 
         char *fPrimer, int fPrimerSize, char *rPrimer, int rPrimerSize,
 	int minDistance, int maxDistance);
 /* Find possible PCR hits.  The fPrimer and rPrimer are on opposite strands.
  * Note: unlike clumps from other query functions, PCR clumps from this 
  * function have already had clump->target->start subtracted from 
  * clump->tStart and clump->tEnd so that the coords are relative to that 
  * target sequence (not the collection of all target sequences). */
 
 #define MAXSINGLEPIECESIZE 5000 /* maximum size of a single piece */
 
-#define gfVersion "36x1"	/* Current BLAT version number */
+#define gfVersion "36x2"	/* Current BLAT version number */
 
 #endif /* GENOFIND_H */