9d9210bb7b34131505ab50b5e62bb88680dc6129
mspeir
  Wed Sep 9 15:14:09 2026 -0700
trackDb docs: add vcfPhasedColorBy, refs #38010

vcfPhasedColorBy has been read by vcfUi.c since the trio display went in, but it
was documented nowhere: not on the VCF help pages, not in trackDbLibrary, and
tdbQuery -check would have rejected it because tagTypes.tab did not list it
either. So a hub author had no way to find the setting and no way to use it
without tripping the checker.

Add the library blurb, the rows in trackDbDoc.html and trackDbHub.v3.html, a
changes.html entry, and the tagTypes.tab registration. The blurb spells out that
mendelDiff needs vcfParentSamples and that function is only offered when
geneTrack is set, since both conditions are enforced in vcfUi.c and neither is
obvious from the value name.

Companion to the two commits documenting the same settings on vcf.html and
hgVcfTrackHelp.html.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/htdocs/goldenPath/help/trackDb/changes.html src/hg/htdocs/goldenPath/help/trackDb/changes.html
index c753c837b11..2feaa5997dc 100755
--- src/hg/htdocs/goldenPath/help/trackDb/changes.html
+++ src/hg/htdocs/goldenPath/help/trackDb/changes.html
@@ -32,30 +32,41 @@
 
 <DIV class="trackDbDoc_intro">
 <H1>Track Database Definition</H1>
 
 <p>This document summarizes the changes to the <a href="trackDbHub.html">UCSC Genome Browser Hub TrackDb specification</a>.<p>
 
 <TABLE class="settingsTable" id="Common_Settings">
 <tbody>
 <tr valign="TOP">
 <th width="100">Date</th>
 <th width="15%">Track Types</th>
 <th width="15%">Link to Doc</th>
 <th>Change</th>
 </tr>
 
+<tr>
+    <td>2026-09-09</td>
+    <td>vcfPhasedTrio</td>
+    <td><a href="trackDbHub.html#vcfPhasedColorBy">vcfPhasedColorBy</a></td>
+    <td>Documenting an existing setting that had never been written down. It picks how
+    variants on each haplotype lane are colored: <code>noColor</code> (the default),
+    <code>deNovo</code> for child variants absent from both parents, <code>mendelDiff</code>
+    for child variants that disagree with the transmitted allele the parents imply, and
+    <code>function</code> for predicted effect on the gene, which also needs
+    <a href="trackDbHub.html#geneTrack">geneTrack</a>.</td>
+</tr>
 <tr>
     <td>2026-09-08</td>
     <td>bigBed</td>
     <td><a href="trackDbHub.html#detailsScript">detailsScript</a></td>
     <td>New plot type <code>scatterPlot</code>, which draws a cloud of background points
     from a JSON or TSV file named by <code>dataUrl</code> and marks the clicked item's own
     coordinates on it. Background points can carry a category, which colors them and builds
     a legend, and a label, which is shown on mouseover. Also new for every plot type: the
     <code>exportFields</code> config key, listing further bigBed fields whose values are
     passed to the module, and hub-relative resolution of any config key ending in
     <code>Url</code>. Such a file is read server-side and must sit inside a connected
     hub.</td>
 </tr>
 <tr>
     <td>2026-09-06</td>