Commits for galt

v398_base to v399_preview (2020-05-11 to 2020-05-18) v399

155197c63e3259d0922c5c3a0e859f4812129db4 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
  • src/blat/blat.c - lines changed 7, context: html, text, full: html, text
  • src/blat/version.doc - lines changed 1, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 8, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 9, context: html, text, full: html, text
  • src/isPcr/isPcr/isPcr.c - lines changed 6, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 19, context: html, text, full: html, text

03ad0cc3681e3a08fa2988990bdea9262faddc24 Mon May 18 00:31:03 2020 -0700

• Added All Results checkbox to hgBlat. Changed it to read tileSize etc from gfserver status so it can use whatever it finds. Correctly shows lengths and required lengths. Instead of limit 20 for dna it now detects min psl->match from genome size. Error messages and warnings should now be complete and correct about suggested and required minimum query lengths. In particular this is motivated by allowing extremely sensitive and short protein and dna queries on Sars-Cov2 (wuhCor1) as well as other microorganisms. refs #25477.
  • src/hg/hgBlat/hgBlat.c - lines changed 225, context: html, text, full: html, text

1a6e86918e3d0c06788e54bb2757ea27072a1fd9 Mon May 18 00:33:59 2020 -0700

• Merge branch 'blatNoSimpRepMask'