155197c63e3259d0922c5c3a0e859f4812129db4
galt
  Sun May 17 17:52:03 2020 -0700
gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477

diff --git src/blat/version.doc src/blat/version.doc
index fe10fbc..c0cc8a7 100644
--- src/blat/version.doc
+++ src/blat/version.doc
@@ -1,22 +1,23 @@
 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.
      o (in 36x3) Added ipv6 support.
      o (in 36x4) Added _alt support.
      o (in 36x5) If ipv6 disabled, retries with ipv4-only socket.
+     o (in 36x6) Added noSimpRepMask option to blat gfServer isPcr to skip simple repeat masking.
 
 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.