353a34ac7e7638457db3f55e57452069113d860b
braney
  Sun Sep 6 13:34:28 2026 -0700
Add a bigNet track type, a net of alignments in a bigBed, refs #20824

Track hubs have had no way to show a real net.  The usual stand-in is a
net rendered as a maf, which loses the level structure that makes a net
useful for establishing orthologous sequence.  bigNet holds the netAlign
columns in a bigBed, so a hub can carry the net itself.

The format is bed6+20: the target in chrom/chromStart/chromEnd, the query
sequence in name, the query strand in strand, then level and the rest of
the netAlign fields.  The trackDb line is

type bigNet <targetDb> <chainTrack>

mirroring type netAlign.  chainTrack is the plain trackDb name of the
bigChain track in the same hub; hgc adds the hub prefix itself.

chainNetLoadRangeHub() builds a chainNet from a bigBed range query and
hands it to the same helpToNet() the SQL path uses, so the nesting is
rebuilt the same way.  netDraw picks its loader off tg->isBigBed and the
drawing code below that is untouched.  genericNetClick does the same for
the details page and follows the named chain track for the alignment.

Also bounds the level walk in helpToNet() by help->maxDepth.  It could
read one past the end of the levels array.

netToBigNet converts a net file to bedToBigBed input.  It writes the tab
line itself rather than calling bigNetTabOut, because autoSql prints a
double with %g and that drops digits off a chain score.

diff --git src/hg/htdocs/goldenPath/help/trackDb/changes.html src/hg/htdocs/goldenPath/help/trackDb/changes.html
index 6bd0d98f46e..f3b99c2075f 100755
--- src/hg/htdocs/goldenPath/help/trackDb/changes.html
+++ src/hg/htdocs/goldenPath/help/trackDb/changes.html
@@ -33,30 +33,42 @@
 
 <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>2026-09-06</td>
+    <td>bigNet</td>
+    <td><a href="trackDbHub.html#bigNet_-_Alignment_Nets">bigNet</a></td>
+    <td>New track type. <code>bigNet</code> holds an alignment net in a bigBed file, so a
+    track hub can show a real net instead of a net rendered as a maf. The type line is
+    <code>type bigNet targetDb chainTrack</code>, where <code>chainTrack</code> names the
+    <a href="/goldenPath/help/bigChain.html">bigChain</a> track in the same hub that holds
+    the alignments. See the <a href="/goldenPath/help/bigNet.html">bigNet format
+    description</a>.</td>
+</tr>
+
 <tr>
     <td>2026-08-31</td>
     <td>bigPsl, bigGenePred, bigBarChart, bigLolly</td>
     <td><a href="trackDbHub.html#searchIndex">searchIndex</a>,
         <a href="trackDbHub.html#searchTrix">searchTrix</a>,
         <a href="trackDbHub.html#mouseOver">mouseOver</a>,
         <a href="trackDbHub.html#mouseOverField">mouseOverField</a>,
         <a href="trackDbHub.html#indelDoubleInsert">indelDoubleInsert</a>,
         <a href="trackDbHub.html#indelQueryInsert">indelQueryInsert</a>,
         <a href="trackDbHub.html#indelPolyA">indelPolyA</a></td>
     <td>Documentation fix, continuing the "For Types" corrections below. Each of these
     settings works on types its entry did not name. <code>searchIndex</code> gains
     <code>bigPsl</code>, <code>bigGenePred</code> and <code>bigBarChart</code>, and
     <code>searchTrix</code> gains <code>bigGenePred</code>; both are read on the
     bigBed-backed search path, whatever the flavor. <code>mouseOver</code> and