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 @@ bigMafSummary.bed file.

The following autoSql definition is used to create the second file, pointed to online with frames <url>. The file mafFrames.as, is pulled in when the bedToBigBed utility is run with the -as=mafFrames.as option.

mafFrames.as

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?"
     )

An example, bedToBigBed -type=bed3+8 -as=mafFrames.as -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb. Another tool, genePredToMafFrames generates the input bigMafFrames.txt file.

Note that the bedToBigBed utility uses a substantial amount of memory: approximately 25% more RAM than the uncompressed BED input file.

@@ -267,21 +267,21 @@

bigBedToBed — converts a bigBed file to ASCII BED format.
bigBedSummary — extracts summary information from a bigBed file.
bigBedInfo — prints out information about a bigBed file.

As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.

Troubleshooting

If you encounter an error when you run the bedToBigBed 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 bedClip program (available here) to remove the problematic row(s) in your input file before running the bedToBigBed program.