75f0d8f409975fddfd9c01378b4404d19393ec6b
hiram
  Fri Sep 25 12:53:35 2026 -0700
beginning to get a miniMap2 process in place refs #34360

diff --git src/hg/utils/automation/mashDistance.pl src/hg/utils/automation/mashDistance.pl
index c6b2caedbc3..cab868050da 100755
--- src/hg/utils/automation/mashDistance.pl
+++ src/hg/utils/automation/mashDistance.pl
@@ -54,32 +54,31 @@
     mashDistance=<float>
     pipeline=minimap2|lastz
     minimapPreset=asm5|asm10|asm20   (only when pipeline=minimap2)
 Any recommendation caveat goes to stderr, not stdout.
 
 options:
     -workDir dir          Fallback scratch dir for mash sketch files, used
                           only for a sequence file that isn't a cacheable
                           GenArk accession (see above).  Default: a fresh
                           directory under /tmp, removed on exit.  Give an
                           existing pipeline's build dir here to reuse/leave
                           behind its mashSketch.{a,b}.msh files.
     -regenerate           Re-sketch and overwrite even if a .msh already
                           exists, cached or fallback.  Use after changing
                           sketch parameters, after a re-built assembly, or
-                          to pick up sketches made before -I <accession>
-                          labeling was added.
+                          some other change to the assembly.
     -dbHost host          Host to run the hgcentraltest dbDb lookup on
                           (see above), default: $dbHost.  hgcentraltest
                           is only reachable from hgwdev -- change this
                           only if you know what you're doing.
     -help                 This help.
 ";
   exit $status;
 }
 
 # Accept an existing path as-is (unchanged, original behavior).  Also
 # accept two "just tell me the name" shorthands and translate them to
 # the standard, already-built location for that assembly -- everything
 # under /gbdb is a fixed, predictable layout, so this is plain path
 # construction, no database lookup needed:
 #   GCA_060551615.1 -> /gbdb/genark/GCA/060/551/615/GCA_060551615.1/GCA_060551615.1.2bit