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/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index e13d50de0c7..3ce64154fb3 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -679,31 +679,31 @@ Defines a number to be added to all coordinates in the annotation track. The default is "0".

maxItems=<#>
Defines the maximum number of items the track can contain. The default value is 10,000. Be aware that tracks with an extremely large number of items can cause system instability. The Kent source utility bedItemOverlapCount can assist in analyzing base overlap with large tracks.

url=<external_url>
Defines a URL for an external link associated with this track. This URL will be used in the details page for the track. Any "$$" in this - string this will be substituted with the item name. There is no default for this attribute.

+ string will be substituted with the item name. There is no default for this attribute.

htmlUrl=<external_url>
Defines a URL for an HTML description page to be displayed with this track. There is no default for this attribute. A template for a standard format HTML track description is here.

bigDataUrl=<external_url>
Defines a URL to the data file for BAM, CRAM, bigBed, bigWig or @@ -941,35 +941,35 @@ example link to show the Chromosome Bands track set to "pack" and added to your view as saved in your cart. Please note that for this feature to work with custom tracks you must use the unique name and identifier number ct_name_#### assigned by our system. You can determine the name for a custom track using the url, https://genome.ucsc.edu/cgi-bin/cartDump.

<trackName>_imgOrd=<number>
vertically orders the tracks on the image based on the numbers provided. You need to specify an order for every visible track when using this parameter
- example link to show two show knownGene track being listed second with gtex first

+ target="_blank">example link to show knownGene track being listed second with gtex first

<trackName>.heightPer=<number>
- sets the height of the a bigWig track + sets the height of a bigWig track in pixels
- example link to set umap bigWig track height to 100 pixels

<trackName>_hideKids=1
hides a specific super track's individual tracks
- example link to hide the Encode Regulation super track

<trackName>_sel=1
selects specific subtrack to be 'checked', allowing display
- example @@ -1104,31 +1104,31 @@ Check for incorrect syntax in the track lines in the annotation file. Be sure that each track line attribute pair consists of the format attribute=attribute name.

Problem:
When I click the submit button, I get the error message "line # of custom input: BED chromStarts[i] must be in ascending order"

Solution:

- This is most likely caused by a logical conflict in the Genome Browse software. It accepts + This is most likely caused by a logical conflict in the Genome Browser software. It accepts custom GFF tracks that have multiple "exons" at the same position, but not BED tracks.
Because the browser translates GFF tracks to BED format before storing the custom track data, GFF tracks with multiple exons will cause an error when the BED is read back in.
To work around this problem, remove duplicate lines in the GFF track.

Problem:
When I click the submit button, the Genome Browser track window displays OK, but my track isn't visible.