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/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
index b902a350567..835ac8a5d49 100755
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
@@ -1432,30 +1432,33 @@
         <div class="format"><code class="level-required">bigDataUrl &lt;url/relativePath&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD class="vcfChildSample"><a name="vcfChildSample"</a><IMG class='toggle detail'>
         <div class="format"><code class="level-full">vcfChildSample &lt;sampleName|altName&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD class="bigDataIndex"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">bigDataIndex &lt;url/relativePath&gt;</code></div>
     </TD></TR>
 
     <TR VALIGN=TOP><TD class="vcfParentSamples"><A NAME="vcfParentSamples"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">vcfParentSamples &lt;sampleName|altName,sampleName|altName&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD class="vcfUseAltSampleNames"><A NAME="vcfUseAltSampleNames"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">vcfUseAltSampleNames &lt;on/off&gt;</code></div>
     </TD></TR>
+    <TR VALIGN=TOP><TD class="vcfPhasedColorBy"><A NAME="vcfPhasedColorBy"><IMG class='toggle detail'>
+        <div class="format"><code class="level-new">vcfPhasedColorBy &lt;mendelDiff|deNovo|function|noColor&gt;</code></div>
+    </TD></TR>
     <TR VALIGN=TOP><TD class="geneTrack"><A NAME="geneTrack"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">geneTrack &lt;track&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD class="vcfDoFilter"><A NAME="vcfDoFilter"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">vcfDoFilter &lt;on/off&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD class="vcfDoQual"><A NAME="vcfDoQual"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">vcfDoQual &lt;on/off&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD class="vcfDoMaf"><A NAME="vcfDoMaf"><IMG class='toggle detail'>
         <div class="format"><code class="level-full">vcfDoMaf &lt;on/off&gt;</code></div>
     </TD></TR>
     <TR VALIGN=TOP><TD>
             <P>Additional settings found in the "Item or
             region tracks" section are also available for displaying