972f44485e27c59335c665585715be63a2d224df
galt
  Thu Oct 1 17:40:11 2020 -0700
Adding timeout for gfServer read and write. Hopefully this will fix both the recent problem from Wuhan killing all our translated blat servers, as well as the mysterious hangs which happen occasionally and end up causing the admins to have to restart the server. refs #26285

diff --git src/blat/version.doc src/blat/version.doc
index 83ad720..aab823a 100644
--- src/blat/version.doc
+++ src/blat/version.doc
@@ -1,24 +1,25 @@
 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.
      o (in 36x7) Fixed compiler optimization issue on mac 2020-06-17 in dlSort().
+     o (in 36x8) Added -timeout option to prevent hanging on blocking input for server read and write.
 
 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.