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/blat/version.doc src/blat/version.doc
index e98f1cb..c514bad 100644
--- src/blat/version.doc
+++ src/blat/version.doc
@@ -1,18 +1,19 @@
-36:
+37:
      o (in 36x1) Fixed problem with -fastMap option that made it put in gaps in the
        allignment sometimes when a short mismatch would be a better choice.
+     o (in 36x2) Fixed problem with -maxIntron set to non-default value on protein query.
 
 36:
      o (in 35x1) added repMatch default values for tileSizes 16 to 18 in genoFind.c
 
 35:
      o (in 34x1) Making total query output reporting a 64 bit number to avoid 
        overflow when people using more than 4 gig of query sequence.
      o (in 34x2) Fixed -out=blast to use +/- instead of -/+ for non-translated.
      o (in 34x3) Fixed -minScore, filter was not working when over half query-size.
      o (in 34x4) Made it convert u's to t's for RNA sequence stuff.
      o (in 34x5) Made gfServer calculate repMatch based on stepSize/tileSize combination the way blat does
        rather than just being good for stepSize 11.
      o (in 34x6) Fixed negative strand pcr psl output
      o (in 34x7) Made it check and error out if the same name is reused in the target database.
      o (in 34x8) Truncate in output PCR primers that dangle off target chrom ends.