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/mouseStuff/chainInfo/chainInfo.c src/hg/mouseStuff/chainInfo/chainInfo.c
index 4ca70a7ec2b..d1c4fb1ef3e 100644
--- src/hg/mouseStuff/chainInfo/chainInfo.c
+++ src/hg/mouseStuff/chainInfo/chainInfo.c
@@ -43,31 +43,31 @@
 };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "chainInfo - parse chains to determine number of introns on query and target\n"
   "usage:\n"
   "   chainInfo query_db target_chrom chainFile syntenicNet.bed target.lst query.lst target_repeatMasker.out query_repeatDir output refGene.tab genePred2.tab genePred3.tab\n"
   "options:\n"
     "    -minGap=N minimum size to be considered a gap (intron).  Default is 60.\n"
     "    -minOverlap=0.N threshold for repeat overlap with gap to be considered a repeat instead of intron.  Default is 0.60.\n"
   "db is query database to match genes to pseudogene\n"
   "chrom is target chromosome to match genes to pseudogene\n"
   "syntenicNet.bed is a filter net file using netFilter -syn converted to bed format\n"
-  "query_repeatDir is the dirctory containing repeatMasker out files chrXX.fa.out\n"
+  "query_repeatDir is the directory containing repeatMasker out files chrXX.fa.out\n"
   "target.lst, query.lst is a list of chromosome names followed by size of each chromosome\n"
   "refGene.tab, genePred2,3 are bed12 files of genes in query database\n"
   );
 }
 
 int qStart(struct chain *chain)
     /* convert coordinates */
 {
     return (chain->qStrand == '+') ? chain->qStart : chain->qSize-chain->qEnd;
 }
 int qEnd(struct chain *chain)
     /* convert coordinates */
 {
     return (chain->qStrand == '+') ? chain->qEnd : chain->qSize-chain->qStart ;
 }