b36887bf67b6569905ba548d189e1fb3e9cb22cc
jcasper
  Thu Mar 6 08:19:11 2025 -0800
Added hic to the list of bigDataUrl filetypes and linked from the hic trackDb
description to the hic help page, refs #35343

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index fb25eb88000..b144c704057 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -385,32 +385,33 @@
 
 <DIV class="yAxisNumLabels"><span class="types bigLolly"></span>
 <div class="format"><code>yAxisNumLabels.&lt;on/off&gt; &lt;integer&gt;</code></div>
     Turn the y axis number labels on or off
 </DIV>
 
 <DIV class="bigDataUrl"><span class="types bigBarChart bigBed bigChain bigInteract bigLolly bigMaf bigPsl bigWig bam hic vcfTabix vcfPhasedTrio"></span>
 <div class="format"><code>bigDataUrl &lt;url/relativePath&gt;</code></div>
     <P class="isRequired">Required: <span class="red">For Hubs</span></P>
     <P>The location of a remote data file containing the bulk of the data for the track.
     This setting is required for all data tracks in a track hub.  </P>  
 <!-- THIS SHOULD BE FIXED for local tracks! -->
     <P>The setting is either the full URL (including <code>http:</code> or another protocol)
     or it is relative to the directory in which the trackDb file containing this setting
     is located.  The file must be in one of
-    the supported remote data file formats: bam/cram, bigBarChart, bigBed, bigChain, bigLolly, bigInteract, bigMaf, bigPsl, bigGenePred, bigNarrowPeak, bigWig or
-    vcfTabix.  Note that bam/cram and vcfTabix/vcfPhasedTrio types require a separate
+    the supported remote data file formats: bam/cram, bigBarChart, bigBed, bigChain, bigLolly,
+    bigInteract, bigMaf, bigPsl, bigGenePred, bigNarrowPeak, bigWig, vcfTabix, or hic.
+    Note that bam/cram and vcfTabix/vcfPhasedTrio types require a separate
     index file that must have the same name as the data file plus a
     standard suffix (".bai" and ".tbi" respectively), unless <A
     <A onclick="jumpTo(this)" HREF="#">bigDataIndex</A> is used.
     All occurrences of the  string <code>$D</code> in the URL will be
     substituted with the genome assembly database name.  This allows a
     trackDb entry to be used with for multiple assemblies.  <code>$D</code>
     substitution is not implemented for track hubs.
 
     </P> <P><B>Example:</B></P>
     <pre>   bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bb</pre>
     &nbsp;&nbsp;or
     <pre>   bigDataUrl biBrainH3K4me1.bb</pre>
 </DIV>
 
 <DIV class="bigDataIndex"><span class="types bam vcfTabix vcfPhasedTrio"></span>
@@ -5386,31 +5387,32 @@
 </DIV>
 
 <DIV class="bigLolly_example"><span class="types bigLolly"></span>
 <div class="format"><B>Example of a bigLolly track</B></div>
 </DIV>
 
 <!-- - - - - - - - hic settings - - - - - - - -->
 <DIV class="hic_intro">
 <H3>hic: Hi-C contact matrices</H3>
     <P>
     The hic track type is for displaying chromatin-chromatin interaction data via heat
 maps.  Currently this track type supports one file format: the .hic file format created
 by the <a href="https://www.aidenlab.org" target="_blank">Aiden Lab</a> at <a target="_blank"
 href="https://www.bcm.edu">Baylor College of Medicine</a>.  This is an indexed
 binary format that supports remote access, so the file can be hosted on any web accessible
-server and displayed at UCSC.
+server and displayed at UCSC.  More details on .hic display at UCSC can be found at the
+<a href="../hic.html">hic help page</a>.
 For more information on the .hic file format and the Juicer tool that generates these files,
 see the documentation on <a target="_blank"
 href="https://github.com/aidenlab/juicer/wiki/Data">github</a>.</p>
 </DIV>
 
 <div class="drawMode"><span class="types hic"></span>
 <div class="format"><code>drawMode &lt;triangle|square|arc&gt;</code></div>
     <p>This setting controls the default display mode for the hic track. In arc
 mode, an interaction between two regions is drawn as an arc between the centers
 of those two regions.  In square mode, interactions are represented by a square
 in a heatmap.  The interacting regions for any square can be identified by
 projecting the sides of the square onto the diagonal axis of the heatmap and
 seeing where those points fall in the chromosome window being viewed.  In
 triangle mode, interactions are drawn as diamonds.  The interaction regions for
 any diamond can be identified by projecting the sides of the diamond onto the