198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/hg/pslPairs/pslPairs.c src/hg/pslPairs/pslPairs.c
index 842a637dafc..31f48851a74 100644
--- src/hg/pslPairs/pslPairs.c
+++ src/hg/pslPairs/pslPairs.c
@@ -42,31 +42,31 @@
 /* Explain usage and exit */
 {
 errAbort(
 "pslPairs - join paired ends in psl alignments\n"
 "usage: pslPairs <pslFile> <pairFile> <pslTableName> <outFilePrefix>\n"
 "  creates: <outFilePrefix>.pairs file\n"
 "  pslFile\t- filtered psl alignments of ends from kluster run\n"
 "  pairFile\t- three column tab separated: forward reverse cloneId\n"
 "\t\t- forward and reverse columns can be comma separated end ids\n"
 "  pslTableName\t- table name the psl alignments have been loaded into\n"
 "  outFilePrefix\t- prefix used for each output file name\n"
 "Options:\n"
 "  -max=N\t- maximum length of clone sequence (default=%d)\n"
 "  -min=N\t- minimum length of clone sequence (default=%d)\n"
 "  -slopval=N\t- deviation from max/min clone lengths allowed for slop report\n\t\t- (default=%d)\n"
-"  -nearTop=N\t- maximium deviation from best match allowed (default=%0.3f)\n"
+"  -nearTop=N\t- maximum deviation from best match allowed (default=%0.3f)\n"
 "  -minId=N\t- minimum pct ID of at least one end (default=%0.2f)\n"
 "  -minOrphanId=N - minimum pct ID for orphan alignment (default=%0.2f)\n"
 "  -tInsert=N\t- maximum insert bases allowed in sequence alignment\n\t\t- (default=%d)\n"
 "  -hardMax=N\t- absolute maximum clone length for long report (default=%d)\n"
 "  -verbose\t- display all informational messages\n"
 "  -noBin\t- do not include bin column in output file\n"
 "  -noRandom\t- do not include placements on random portions\n\t\t- {length(chr name) < 7}\n"
 "  -slop\t\t- create <outFilePrefix>.slop file of pairs that fall within\n\t\t- slop length\n"
 "  -short\t- create <outFilePrefix>.short file of pairs shorter than\n\t\t- min size\n"
 "  -long\t\t- create <outFilePrefix>.long file of pairs longer than\n\t\t- max size, but less than hardMax size\n"
 "  -mismatch\t- create <outFilePrefix>.mismatch file of pairs with\n\t\t- bad orientation of ends\n"
 "  -orphan\t- create <outFilePrefix>.orphan file of unmatched end sequences",
 MAX, MIN, SLOPVAL, NEARTOP, MIN_ID, MIN_ORPHAN_ID, TINSERT, HARDMAX
 );
 }