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/hubQuickStartGroups.html src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html index 0d1b8e46b04..65a284bab95 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html @@ -122,31 +122,31 @@ <pre><code><strong>track</strong> <em>uniqueCompositeTrackName</em> <strong>compositeTrack</strong> <em>on</em> ... <strong>track</strong> <em>uniqueNameWithoutSpaces</em> <strong>parent</strong> <em>uniqueCompositeTrackName on</em> ... <strong>track</strong> <em>newUniqueNameWithoutSpaces</em> <strong>parent</strong> <em>uniqueCompositeTrackName off</em> </code></pre> <p> A composite track groups together related tracks, usually but not necessarily of a similar type, that you want to display together (referred to as "subtracks"). If you want to organize tracks into a hierarchy and there is a single level of grouping, use a composite. For example, you could group together called variants or ChIP-seq peaks with their underlying BAM reads or sequencing coverage. The <code><strong>compositeTrack</strong> on</code> line defines the parent track that will be later referenced as <code><strong>parent</strong> uniqueCompositeTrackName off</code> in each subtrack's -stanza. Either "on" or "off" can be used to set a subtrack to be displayed or not +stanza. Either "on" or "off" can be used to set a subtrack to be displayed or not displayed by default. Composite tracks can be broken apart further to group very similar tracks with the trackDb use of <a href="trackDb/trackDbHub.html#subGroups" target="_blank">subGroups</a> and <a href="trackDb/trackDbHub.html#view" target="_blank">views</a>, not demonstrated here. Read <a href="trackDb/trackDbHub.html#Composite_Track_Settings" target="_blank">all about composite tracks here</a>. See an <a href="http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hg19/trackDb.txt" target="_blank">example trackDb.txt</a>.</p> <!-- ========== supertracks ==================== --> <a name="superTrack"></a><br> <h2>Understanding supertracks</h2> <pre><code><strong>track</strong> <em>uniqueSuperTrackName</em> <strong>superTrack</strong> <em>on show</em> ... @@ -171,31 +171,31 @@ For example, you could have a composite with RNA-seq results and a composite with ChIP-Seq results grouped together into a supertrack describing a cell line. Supertracks contain composite tracks or container multiWigs, but not vice versa. The <code><strong>superTrack</strong> on show</code> line allows for this track to be later referenced as <code><strong>parent</strong> uniqueSuperTrackName</code> in each of the children subtracks (note how it is only required for direct children, and not for subtracks contained in a composite inside the supertrack -more below). The "show" is optional and sets the supertrack to display by default. It may help to think of the original declaring supertrack stanza as a light switch that by default is off, and can be flipped on by adding show.</p> <p> All tracks that claim membership to the supertrack can then set their own visibilities in lower stanzas by declaring settings such as by having the parent line and a separate <code>visibility dense</code> line. If no visibility setting is defined for a track, the default setting of hide is assigned. This can cause confusion if one -mistakenly tries to set visibilities only at the top parent supertack stanza and +mistakenly tries to set visibilities only at the top parent supertrack stanza and leaves out visibility declarations for all children.</p> <p> Also do not confuse the parent line with how it is used in composites. For example, in supertracks DO NOT try something like <strike><code>parent uniqueSuperTrackName [off/on]</code></strike>, where the <code>[off/on]</code> will only work with composite tracks. In the above nested example you do see <code>track uniqueNameWithoutSpaces</code> with a setting line specific only to the fact it is a child of a composite, <code><strong>parent</strong> <em>uniqueCompositeTrackNameInSuperTrack on</em></code>. The parent -of the child composite track is in turn is a child to a supertrack declared by +of the child composite track is in turn a child to a supertrack declared by <code><strong>parent</strong> <em>uniqueSuperTrackName</em></code>. Read <a href="trackDb/trackDbHub.html#superTrack" target="_blank">all about supertracks here</a>. See an <a href="http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGroupings/hg19/trackDb.txt" target="_blank">example trackDb.txt</a>.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->