37adfded75ec133c1fd2b4cb86e4757e76a54de5
mspeir
  Wed Sep 9 15:29:55 2026 -0700
trackDb docs: describe minAc and vcfDoMinAc, and fix two mislabelled vcfDoMaf rows, refs #38010

The last two VCF settings with no description anywhere. Both were absent from
trackDbLibrary, trackDbDoc and trackDbHub.v3, so registering them in
tagTypes.tab last commit made them legal but still undiscoverable.

minAc is a real filter, not just a UI default: minAcFail() in vcfTrack.c takes
the largest alternate allele count from the AC field of the INFO column and
drops the record when it is below the setting. Records whose INFO has no usable
AC are never dropped, which is worth saying since it is the surprising half.
vcfDoMinAc gates the matching control, like its three siblings.

Rows follow the placement the sibling settings already use: minAc beside
minFreq in the vcfTabix table, vcfDoMinAc beside vcfDoMaf in both the vcfTabix
and vcfPhasedTrio tables.

While adding those, trackDbDoc.html turned out to carry two rows with
class="vcfDoMaf" whose anchor and format line both read vcfDoQual, so the page
listed vcfDoQual twice and never showed vcfDoMaf's syntax. Copy-paste, present
in both the vcfTabix and vcfPhasedTrio tables. Corrected.

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 2feaa5997dc..b2071d564b3 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>vcf, vcfTabix, vcfPhasedTrio</td>
+    <td><a href="trackDbHub.html#minAc">minAc</a></td>
+    <td>Documenting two more existing settings. <code>minAc</code> hides a variant whose
+    alternate allele count, read from the AC field of the INFO column, falls below the given
+    number; variants with no usable AC are always shown.
+    <a href="trackDbHub.html#vcfDoMinAc">vcfDoMinAc</a> turns the matching filter control on
+    the configuration page on or off. Neither was listed in tagTypes.tab, so until now
+    <code>tdbQuery -check</code> rejected both.</td>
+</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>