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/lib/vcf.c src/lib/vcf.c
index db148b4225f..3db0767f942 100644
--- src/lib/vcf.c
+++ src/lib/vcf.c
@@ -1597,31 +1597,31 @@
         "\"The fields of a Variant Call Format data line\""
         "    ("
         "    string chrom;      \"An identifier from the reference genome\""
         "    uint pos;          \"The reference position, with the 1st base having position 1\""
         "    string id;         \"Semi-colon separated list of unique identifiers where available\""
         "    string ref;                \"Reference base(s)\""
         "    string alt;                \"Comma separated list of alternate non-reference alleles "
                                          "called on at least one of the samples\""
         "    string qual;       \"Phred-scaled quality score for the assertion made in ALT. i.e. "
                                  "give -10log_10 prob(call in ALT is wrong)\""
         "    string filter;     \"PASS if this position has passed all filters. Otherwise, a "
                                   "semicolon-separated list of codes for filters that fail\""
         "    string info;       \"Additional information encoded as a semicolon-separated series "
                                  "of short keys with optional comma-separated values\""
         "    string format;     \"If genotype columns are specified in header, a "
-                                 "semicolon-separated list of of short keys starting with GT\""
+                                 "semicolon-separated list of short keys starting with GT\""
         "    string genotypes;  \"If genotype columns are specified in header, a tab-separated "
                                  "set of genotype column values; each value is a colon-separated "
                                  "list of values corresponding to keys in the format column\""
         "    )";
 
 struct asObject *vcfAsObj()
 // Return asObject describing fields of VCF
 {
 return asParseText(vcfDataLineAutoSqlString);
 }
 
 char *vcfGetSlashSepAllelesFromWords(char **words, struct dyString *dy)
 /* Overwrite dy with a /-separated allele string from VCF words,
  * skipping the extra initial base that VCF requires for indel alleles if necessary,
  * and trimming identical bases at the ends of all alleles if there are any.