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/htdocs/goldenPath/help/bigMaf.html src/hg/htdocs/goldenPath/help/bigMaf.html
index 6f62e5c5b9c..e1c365a9a59 100755
--- src/hg/htdocs/goldenPath/help/bigMaf.html
+++ src/hg/htdocs/goldenPath/help/bigMaf.html
@@ -72,31 +72,31 @@
 <code>bigMafSummary.bed</code> file.</p>
 <p>
 The following autoSql definition is used to create the second file,
 pointed to online with <code>frames &lt;url&gt;</code>. The file
 <a href="examples/mafFrames.as"><em>mafFrames.as</em></a>, is pulled in when
 the <code>bedToBigBed</code> utility is run with the <code>-as=mafFrames.as</code>
 option.</p>
 <h6>mafFrames.as</h6>
 <pre><code>table mafFrames
 "codon frame assignment for MAF components"
     (
     string chrom;      "Reference sequence chromosome or scaffold"
     uint   chromStart; "Start range in chromosome"
     uint   chromEnd;   "End range in chromosome"
     string src;        "Name of sequence source in MAF"
-    ubyte frame;       "frame (0,1,2) for first base(+) or last bast(-)"
+    ubyte frame;       "frame (0,1,2) for first base(+) or last base(-)"
     char[1] strand;    "+ or -"
     string name;       "Name of gene used to define frame"
     int    prevFramePos;  "target position of the previous base (in transcription direction) that continues this frame, or -1 if none, or frame not contiguous"
     int    nextFramePos;  "target position of the next base (in transcription direction) that continues this frame, or -1 if none, or frame not contiguous"
     ubyte  isExonStart;  "does this start the CDS portion of an exon?"
     ubyte  isExonEnd;    "does this end the CDS portion of an exon?"
     )</code></pre>
 <p>
 An example, <code>bedToBigBed -type=bed3+8 -as=mafFrames.as
 -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb</code>. Another tool,
 <code>genePredToMafFrames</code> generates the input
 <code>bigMafFrames.txt</code> file.</p>
 <p>
 Note that the <code>bedToBigBed</code> utility uses a substantial amount of memory: approximately 
 25% more RAM than the uncompressed BED input file.</p>
@@ -267,21 +267,21 @@
 <ul>
   <li>
   <code>bigBedToBed</code> &mdash; converts a bigBed file to ASCII BED format.</li>
   <li>
   <code>bigBedSummary</code> &mdash; extracts summary information from a bigBed file.</li>
   <li>
   <code>bigBedInfo</code> &mdash; prints out information about a bigBed file.</li>
 </ul>
 <p>
 As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the 
 command line to view the usage statement.</p>
 
 <h2>Troubleshooting</h2>
 <p>
 If you encounter an error when you run the <code>bedToBigBed</code> program, check your input 
-file for data coordinates that extend past the the end of the chromosome. If these are present, run 
+file for data coordinates that extend past the end of the chromosome. If these are present, run 
 the <code>bedClip</code> program 
 (<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">available here</a>) to remove the problematic
 row(s) in your input file before running the <code>bedToBigBed</code> program.</p> 
 
 <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->