1c07e6e9103123809e420560f2ebf370dde996ea
jcasper
  Sun Jan 11 21:24:24 2026 -0800
Docs for the hicArcLimit and hicArcLimitEnabled setings, which control how many arcs
are actually drawn in arc mode, refs #36774

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index 50a7f4c7dfd..fd12de9a664 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -5501,30 +5501,51 @@
 is applied.
     </p>
 </div>
 
 <div class="hicDistanceMax"><span class="types hic"></span>
 <div class="format"><code>hicDistanceMax &lt;integer&gt;</code></div>
     <p>Hi-C tracks have a setting that controls the maximum interaction distance
 in nucleotides for the heatmap.  If a portion of the heatmap represents an interaction
 farther than the value of the maximum distance setting, that portion of the heatmap simply
 isn't drawn.  This setting, hicDistanceMax, controls the default value for that
 maximum (without this setting, the default is 0).  A value of 0 means that no filter
 is applied.
     </p>
 </div>
 
+<div class="hicArcLimit"><span class="types hic"></span>
+<div class="format"><code>hicArcLimit &lt;integer&gt;</code></div>
+    <p>The "arc" display mode for Hi-C tracks can become difficult to read if too many
+arcs are being drawn, particularly if many of them have scores close to the saturation
+score.  This setting can be used to restrict the display to only the N highest scoring
+arcs (it has no effect in other display modes).  The companion setting, hicArcLimitEnabled,
+controls whether this filter is applied to the track by default or not.  The default
+value for this setting is 10000.
+    </p>
+</div>
+
+<div class="hicArcLimitEnabled"><span class="types hic"></span>
+<div class="format"><code>hicDistanceMax &lt;true|false&gt;</code></div>
+    <p>The "arc" display mode for Hi-C tracks can become difficult to read if too many
+arcs are being drawn, so there is an option to limit the display to the N highest scoring
+interactions.  The value of N is controlled by the companion setting, hicArcLimit, while
+this setting controls whether the filter is automatically turned on when the track is
+loaded.  The default value is false.
+    </p>
+</div>
+
 <DIV class="hic_example"><span class="types hic"></span>
 <div class="format"><B>Example of a hic track</B></div>
     <pre>
     track myHiCData
     type hic
     drawMode arc
     color 0,0,255
     saturationScore 12
     normalization KR
     bigDataUrl http://...
     </pre>
 </div>
 
 
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