160d10a30597d7435c30409878e2ba11c3e7c660
mspeir
Wed Sep 9 14:19:40 2026 -0700
trackDb docs: stop the shared script from aborting on the pages without a search box, refs #38062
Two JavaScript faults on the trackDb doc pages, both of which trackDbHub.v3.html
had already avoided while the other pages drifted.
trackDbDoc.html, changes.html and trackDbHub.v0/v1/v2.html load /js/utils.js in
their head, and the hgMenubar include further down brings in the same file by a
different path, so it ran twice. utils.js declares mouseoverContainer with let
at top level, so the second run threw a redeclaration error. v3 does not load
utils.js in the head, and the menubar copy is in place well before anything
needs it, so drop the head copy from the other five.
documentLoad() then called addEventListener on the result of
getElementById("tdbSearch") with no null check, and only v3 has that input, so
the function threw partway through on the other four pages and never reached
its end. The search box and jump-to-top button do not exist on those pages, so
nothing visible was lost, but the exception aborted the rest of documentLoad
and would have swallowed anything added after it. Guard the two listeners.
All six pages now load with no console errors, checked in a browser.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
index 4eb5f19adf9..21724305fec 100755
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
@@ -1,835 +1,834 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1">
<META name="description" content="UCSC Track Database Definition">
<META name="keywords" content="tracDb, tracks, UCSC, bioinformatics">
<TITLE>UCSC Track Database Definition</TITLE>
<LINK REL="STYLESHEET" HREF="/style/HGStyle.css">
<LINK REL="STYLESHEET" HREF="trackDbDoc.css">
<script type="text/javascript" src="/js/jquery.js"></script>
<script type="text/javascript" src="/js/staticDoc.js"></script>
- <script type="text/javascript" src="/js/utils.js"></script>
<script type="text/javascript" src="trackDbDoc.js"></script>
<script type="text/javascript">
$(document).ready(function() {
//tdbDoc.library.checkup(); // Run this test during development only
// TOC Self assembly EXPERIMENTAL
tdbDoc.tocAssemble( 0, ["bed_flavors","parent_supertrack",
"parent_view","parent_container"] );
tdbDoc.documentLoad();
});
</script>
</HEAD>
<BODY>
<A NAME="TOP"></A>
<!-- Format everthing inside this narrower "pageWidth" window -->
<div class="pageWidth">
<IMG SRC="/images/title.jpg">
<!--#include virtual="../../../cgi-bin/hgMenubar"-->
<!--Content Tables-->
<!--outer table is for border purposes-->
<div class="contentBorder">
<div class="lightBlueBar">
<div class="lightBlueBarTitle"> Track Database Definition</div>
</div>
<!-- Finally to the content -->
<div class="borderGuard">
<DIV class="trackDbHub_intro">
<H1>Hub Track Database Definition (<SPAN id="trackDbHub_version">v1</SPAN>)</H1>
<H2>How to declare Dataset Display Settings in Genome Browser Hubs</H2>
<P>This document describes how to set dataset display characteristics
using "track database" or "trackDb" settings through key-value pair
associations used in a Track Hub's trackDb.txt file.
<P>The text file format for trackDb settings starts by creating a
text block, or "stanza", for each track dataset following
"ra" rules to establish a "record" of related settings. The first
line establishes the <code>track</code> "key", with additional lines
containing further "setting" keys, and one or more words or numbers
that follow, which are the "values" for each setting. All trackDb
stanzas are keyed by <code>track</code> and delimited by blank lines.
Here is an example:</P>
<pre>
track myFirstTrack
type bigBed 3
bigDataUrl myFirstTrack.bb
shortLabel Example Data
longLabel The data in this track is format "bigBed 3". </pre>
<P>A basic track stanza should have these five above settings
(<code>track type bigDataUrl shortLabel longLabel</code>).
The first line's <code>track</code> key value (<code>myFirstTrack</code>) is the
identifier for the dataset given to the Browser and it must be
unique for each track within your data hub. After the <code>track</code> key,
the most important setting is the <code>type</code> key. This value
(<code>bigBed 3</code>) tells the Browser the type of format the
data is in, defines how to display it, and determines
which options are available for fine control of that display.
</P>
<P>While there are over 100 settings (providing a high level of flexibility for track
display) defined in this document and supported at UCSC, only the above five
are <font class="level-required">required</font>
to define a track and other sites that display hubs have more limited settings support.
To ease the task of hub developers and sites that
display hubs, each setting has been assigned a support level. The most
commonly used and broadly supported settings have
been designated as <font class="level-base">base</font> settings, to foster
hub portability. The level for each setting is indicated in this document by
color, shown below and in each description
section as well as in the <A HREF="#toc">Table of Contents</A>.
The support levels are:
<table style="margin-left: 50px;">
<tr><td class="level-required">required</td><td>required settings</td></tr>
<tr><td class="level-base">base</td><td>common settings supported
at other sites</td></tr>
<tr><td class="level-deprecated">deprecated</td><td>settings that
are being retired (replacement is listed in details section)</td></tr>
<tr><td class="level-new">new</td><td>new settings not yet assigned
a level (may be replaced)</td></tr>
<tr><td class="level-full">full</td><td>other settings</td></tr>
</table>
</P>
<P>This documentation page has also been assigned a version number
so that when <font class="level-new">new</font> settings are added, or
older settings are <font class="level-deprecated">deprecated</font>
other browser sites and track hub builders can verify the hub to
the relevant version.
</P>
</DIV>
<P>The remainder of this document is divided into the following sections and should be
used as a ready reference.</P>
<IMG class='toggle all' /> <I>Expand/close descriptions of settings
in the sections below.</I>
<OL>
<LI><A HREF="#commonSettings">Common trackDb settings</A></LI>
<LI><A HREF="#settingsByType">Settings by track type</A> – with examples
<UL>
<LI><A HREF="#bigBed_-_Item_or_Region_Track_Settings">bigBed</A>:
Item or region tracks</LI>
<LI><A HREF="#bigWig_-_Signal_Graphing_Track_Settings">bigWig</A>:
Signal graphing tracks</LI>
<LI><A HREF="#bam">bam/cram</A>: Compressed Sequence Alignment/Map tracks</LI>
<LI><A HREF="#vcfTabix">vcfTabix</A>: Variant Call Format</LI>
</UL></LI>
<LI><A HREF="#groupingTracks">Grouping tracks into sets and hierarchies</A>
– with examples
<UL>
<LI><A HREF="#superTrack">Supertracks (Folders)</A></LI>
<LI><A HREF="#compositeTrack">Composite Tracks</A>
<UL>
<LI><A HREF="#subGroups">Subgroups</A></LI>
<LI><A HREF="#view">Views</A></LI>
</UL></LI>
<LI><A HREF="#aggregate">Aggregate or Overlay Tracks: multiWig</A></LI>
</UL></LI>
<LI><A HREF="#toc">Table of Contents</A></LI>
</OL>
</div></div>
<!-- Settings specification -->
<div id="specification">
<!-- Next section -->
<div class="contentBorder">
<A name="commonSettings"></A>
<div class="lightBlueBar">
<div class="lightBlueBarTitle"> Common trackDb settings</div>
</div>
<div class="borderGuard">
<TABLE class="settingsTable" id="Common_Settings">
<THEAD><TR><TD><DIV ID="commonSettings_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection' /> Common Settings</TH></TR>
<TR VALIGN=TOP><TD class="track"><A name="track"></A><IMG class='toggle detail'>
<div class="format"><code class="level-required">track</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="type"><A name="type"></A><IMG class='toggle detail'>
<div class="format"><code class="level-required">type</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="shortLabel"><A name="shortLabel"></A><IMG class='toggle detail'>
<div class="format"><code class="level-required">shortLabel</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="longLabel"><A name="longLabel"></A><IMG class='toggle detail'>
<div class="format"><code class="level-required">longLabel</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataUrl"><A name="bigDataUrl"></A><IMG class='toggle detail'>
<div class="format"><code class="level-required">bigDataUrl <url/relativePath></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="html"><A name="html"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">html</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="visibility"><A name="visibility"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">visibility</code></div>
</TD></TR>
</TABLE>
<BR>
<A name="commonLessFrequent"></A>
<TABLE class="settingsTable" id="Common_Settings_-_less_frequent">
<THEAD><TR><TD><DIV ID="lessCommon_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH>
<IMG class='toggle oneSection' /> Common Optional Settings
</TH> </TR>
<TR VALIGN=TOP><TD class="color"><A name="color"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">color <red,green,blue></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="priority"><A name="priority"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">priority <float></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="altColor"><A name="altColor"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">altColor <red,green,blue></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="boxedCfg"><A name="boxedCfg"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">boxedCfg <on/off></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="chromosomes"><A name="chromosomes"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">chromosomes <chr1,chr2,...></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="darkerLabels"><A name="darkerLabels"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-new">darkerLabels on</code><BR>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="dataVersion"><A name="dataVersion"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">dataVersion <str></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="directUrl_for_hubs">
<A name="directUrl"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">directUrl <url></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="iframeUrl"><A name="iframeUrl"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">iframeUrl <url></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="iframeOptions"><A name="iframeOptions"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">iframeOptions <string></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="mouseOverField"><A name="mouseOverField"></A><IMG class='toggle detail'>
<div class="format"><code class="level-new">mouseOverField <fieldName></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="otherDb"><A name="otherDb"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">otherDb <otherDb></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="pennantIcon"><A name="pennantIcon"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">pennantIcon <icon> [html [tip]]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="url_for_hubs">
<A name="url"></A>
<A name="urlLabel"></A><IMG class='toggle detail'>
<div class="format">
<span class="url"><code class="level-full">url <url></code></span><BR>
<span class="urlLabel"><code class="level-full">urlLabel <label></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="urls"><A name="urls"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-full">urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...</code><BR>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="skipEmptyFields"><A name="skipEmptyFields"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-new">skipEmptyFields on</code><BR>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="skipFields"><A name="skipFields"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-new">skipFields fieldName1,fieldName2 ...</code><BR>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="sepFields"><A name="sepFields"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-new">sepFields fieldName1,fieldName2 ...</code><BR>
</div>
</TD></TR>
</TABLE>
</div></div>
<!-- Next section -->
<div class="contentBorder">
<A name="settingsByType"></A>
<div class="lightBlueBar">
<div class="lightBlueBarTitle"> Settings by track type</div>
</div>
<div class="borderGuard">
<P>Many settings are
valid only for certain types of tracks. Many of these tracks
are described below along with settings specific to their types.</P>
<A name="bigBed"></A>
<TABLE class="settingsTable" id="bigBed_-_Item_or_Region_Track_Settings">
<THEAD><TR><TD><DIV ID="bigBed_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
bigBed - Item or region track settings
</TH></TR>
<TR VALIGN=TOP><TD class="bigBed"><IMG class='toggle detail'>
<div class="format">
<code>type bigBed <3-12> [+/.]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'>
<div class="format"><code class="level-required">bigDataUrl <url/relativePath></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="itemRgb"><A name="itemRgb"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">itemRgb on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="colorByStrand"><A name="colorByStrand"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">colorByStrand <red,green,blue>
<red,green,blue></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="denseCoverage"><A name="denseCoverage"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">denseCoverage <maxVal></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="labelOnFeature"><A name="labelOnFeature"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">labelOnFeature <on/off></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="exonArrows"><A name="exonArrows"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">exonArrows <on/off></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="exonNumbers"><A name="exonNumbers"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">exonNumbers <on/off></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="scoreFilter">
<A name="scoreFilter"></A>
<A name="scoreFilterLimits"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-full">scoreFilter <low>[:<high>]</code><BR>
<span class="scoreFilterLimits"><code class="level-full">scoreFilterLimits <low>[:<high>]</code></span><BR>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="maxItems"><A name="maxItems"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">maxItems <integer></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="maxWindowToDraw">
<A name="maxWindowToDraw"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">maxWindowToDraw <integer></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="minGrayLevel"><A name="minGrayLevel"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">minGrayLevel <1-9></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="noScoreFilter"><A name="noScoreFilter"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">noScoreFilter on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="spectrum">
<A name="spectrum"></A>
<A name="scoreMax"></A>
<A name="scoreMin"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-full">spectrum on</code><BR>
<span class="scoreMax"><code class="level-full">scoreMax <integer></code></span><BR>
<span class="scoreMin"><code class="level-full">scoreMin <integer></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="thickDrawItem"><A name="thickDrawItem"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">thickDrawItem <off/on></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="searchIndex"><A name="searchIndex"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">searchIndex <str></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="searchTrix"><A name="searchTrix"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">searchTrix <url/relativePath></code></div>
</TD></TR>
</TABLE>
<TABLE class="settingsTable" id="Item_or_Region_Track_Settings_-_less_frequent">
<TR VALIGN=TOP><TH><A name="item_lessFrequent"></A>
<IMG class='toggle oneSection' /> Less frequently used item track settings
</TH></TR>
<TR VALIGN=TOP><TD class="bedNameLabel"><A name="bedNameLabel"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">bedNameLabel <label></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="exonArrowsDense">
<A name="exonArrowsDense"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">exonArrowsDense <off/on></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="itemImagePath">
<A name="itemImagePath"></A>
<A name="itemBigImagePath"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">itemImagePath <path> <suffix></code><BR>
<span class="itemBigImagePath"><code class="level-full">itemBigImagePath <path> <suffix></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="linkIdInName"><A name="linkIdInName"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">linkIdInName on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="nextExonText">
<A name="nextExonText"></A>
<A name="prevExonText"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-full">nextExonText <str></code><BR>
<span class="prevExonText"><code class="level-full">prevExonText <str></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="scoreLabel"><A name="scoreLabel"></A><IMG class='toggle detail'>
<div class="format"><code class="level-new">scoreLabel <label></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="showTopScorers">
<A name="showTopScorers"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">showTopScorers #</code></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="bigBed_example">
<A name="bigBed_Examples"></A><IMG class='toggle detail'>
<div class="format"><B>Examples of item base types</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="bigWig">
<TABLE class="settingsTable" id="bigWig_-_Signal_Graphing_Track_Settings">
<THEAD><TR><TD><DIV ID="bigWig_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
bigWig - Signal graphing track settings
</TH></TR>
<TR VALIGN=TOP><TD class="bigWig"><IMG class='toggle detail'>
<div class="format">
<code>type bigWig <#> <#></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="autoScale"><A name="autoScale"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">autoScale <off/on></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="maxHeightPixels">
<A name="maxHeightPixels"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">maxHeightPixels <max:default:min></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="viewLimits">
<A name="viewLimits"></A>
<A name="viewLimitsMax"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-base">viewLimits <lower:upper></code><BR>
<span class="viewLimitsMax"><code class="level-full">viewLimitsMax <lower:upper></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="alwaysZero"><A name="alwaysZero"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">alwaysZero <off/on></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'>
<div class="format"><code class="level-full">bigDataUrl <url/relativePath></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="graphTypeDefault">
<A name="graphTypeDefault"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">graphTypeDefault points</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="maxWindowToQuery">
<A name="maxWindowToQuery"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">maxWindowToQuery <integer></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="negateValues">
<A name="negateValues"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">negateValues <on></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="smoothingWindow">
<A name="smoothingWindow"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">smoothingWindow <off/1-16></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="transformFunc">
<A name="transformFunc"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">transformFunc <NONE/LOG></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="windowingFunction">
<A name="windowingFunction"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">windowingFunction
<mean/mean+whiskers/maximum/minimum></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="yLineMark">
<A name="yLineMark"></A>
<A name="yLineOnOff"></A>
<A name="gridDefault"></A><IMG class='toggle detail'>
<div class="format">
<span class="yLineMark"><code class="level-full">yLineMark <#></code></span><BR>
<span class="yLineOnOff"><code class="level-full">yLineOnOff <off/on></code></span><BR>
<span class="gridDefault"><code class="level-full">gridDefault on</code></span></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="bigWig_example"><IMG class='toggle detail'>
<div class="format"><B>Examples of signal graphing tracks</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="bam"></A>
<TABLE class="settingsTable" id="bam_-_Compressed_Alignment_Track_Settings">
<THEAD><TR><TD><DIV ID="bam_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
bam/cram - Compressed Sequence Alignment track settings</TH></TR>
<TR VALIGN=TOP><TD class="bam"><IMG class='toggle detail'>
<div class="format"><code>type bam</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'>
<div class="format"><code class="level-required">bigDataUrl <url/relativePath></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataIndex"><IMG class='toggle detail'>
<div class="format"><code class="level-full">bigDataIndex <url/relativePath></code></div>
</TD></TR>
<TR class="related1st" VALIGN=TOP><TD class="bamColorMode">
<A name="bamColorMode"></A><IMG class='toggle detail setD'>
<div class="format"><I>Related settings:</I><BR>
<code class="level-full">bamColorMode <strand/gray/tag/off></code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="bamGrayMode">
<A name="bamGrayMode"></A>
<A name="aliQualRange"></A>
<A name="baseQualRange"></A><IMG class='toggle detail setD'>
<div class="format">
<code class="level-full">bamGrayMode <aliQual/baseQual/unpaired></code><BR>
<span class="aliQualRange"><code class="level-full">aliQualRange <min:max></code></span><BR>
<span class="baseQualRange"><code class="level-full">baseQualRange <min:max></code><</span></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="bamColorTag">
<A name="bamColorTag"></A><IMG class='toggle detail setD'>
<div class="format"><code class="level-full">bamColorTag <XX></code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="noColorTag">
<A name="noColorTag"></A><IMG class='toggle detail setD'>
<div class="format"><code class="level-full">noColorTag .</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bamSkipPrintQualScore"><A name="bamSkipPrintQualScore"></A>
<IMG class='toggle detail'>
<div class="format"><code class="level-full">bamSkipPrintQualScore .</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="indelDoubleInsert">
<A name="indelDoubleInsert"></A>
<A name="indelQueryInsert"></A>
<A name="indelPolyA"></A><IMG class='toggle detail'>
<div class="format">
<span class="indelDoubleInsert"><code class="level-full">indelDoubleInsert <off/on></code></span><BR>
<span class="indelQueryInsert"><code class="level-full">indelQueryInsert <off/on></code></span><BR>
<span class="indelPolyA"><code class="level-full">indelPolyA <off/on></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="minAliQual"><A name="minAliQual"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">minAliQual <#></code></div>
</TD></TR>
<TR class="related1st" VALIGN=TOP><TD class="pairEndsByName">
<A name="pairEndsByName"></A><IMG class='toggle detail setE'>
<div class="format"><I>Related settings:</I><BR>
<code class="level-full">pairEndsByName .</code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="pairSearchRange">
<A name="pairSearchRange"></A><IMG class='toggle detail setE'>
<div class="format"><code class="level-full">pairSearchRange <#></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="showNames"><A name="showNames"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">showNames <on/off></code></div>
</TD></TR>
<TR VALIGN=TOP><TD>
<P>Additional settings
found in the "Item or region tracks" section are also
available for displaying bam tags.</P>
<A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>,
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="bam_example"><IMG class='toggle detail'>
<div class="format"><B>Example of a bam track</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="vcfTabix"></A>
<TABLE class="settingsTable" id="vcfTabix_-_Variant_Call_Format_Track_Settings">
<THEAD><TR><TD><DIV ID="vcfTabix_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'/>
vcfTabix - Variant Call Format (indexed by tabix) track settings
</TH></TR>
<TR VALIGN=TOP><TD class="vcfTabix"><IMG class='toggle detail'>
<div class="format"><code>type vcfTabix</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataUrl"><IMG class='toggle detail'>
<div class="format"><code class="level-required">bigDataUrl <url/relativePath></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="bigDataIndex"><IMG class='toggle detail'>
<div class="format"><code class="level-full">bigDataIndex <url/relativePath></code></div>
</TD></TR>
<TR class="related1st" VALIGN=TOP><TD class="hapClusterEnabled"><A NAME="hapClusterEnabled"><IMG class='toggle detail setF'>
<div class="format"><I>Related settings:</I><BR>
<code class="level-full">hapClusterEnabled <true|false></code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="hapClusterColorBy"><A NAME="hapClusterColorBy"><IMG class='toggle detail setF'>
<div class="format"><code class="level-full">hapClusterColorBy <altOnly|refAlt|base></code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="hapClusterTreeAngle"><A NAME="hapClusterTreeAngle"><IMG class='toggle detail setF'>
<div class="format"><code class="level-full">hapClusterTreeAngle <triangle|rectangle></code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="hapClusterHeight"><A NAME="hapClusterHeight"><IMG class='toggle detail setF'>
<div class="format"><code class="level-full">hapClusterHeight <N></code></div>
</TD></TR>
<TR class="related1st" VALIGN=TOP><TD class="applyMinQual"><A NAME="applyMinQual"><IMG class='toggle detail setG'>
<div class="format"><I>Related settings:</I><BR>
<code class="level-full">applyMinQual <true|false></code></div>
</TD></TR>
<TR class="related" VALIGN=TOP><TD class="minQual"><A NAME="minQual"><IMG class='toggle detail setG'>
<div class="format"><code class="level-full">minQual <<EM>Q</EM>></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="minFreq"><A NAME="minFreq"><IMG class='toggle detail'>
<div class="format"><code class="level-full">minFreq <<EM>F</EM>></code></div>
</TD></TR>
<TR VALIGN=TOP><TD>
<P>Additional settings found in the "Item or
region tracks" section are also available for displaying
Variant Call Format tracks.</P>
<A onclick="return jumpTo(this);" HREF="#">maxWindowToDraw</A>
</DIV>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="vcfTabix_example">
<IMG class='toggle detail'>
<div class="format"><B>Example of a VCF track</B></div>
</TD></TR>
</TABLE>
<BR><BR>
</div></div>
<!-- Next section -->
<div class="contentBorder">
<A name="groupingTracks"></A>
<div class="lightBlueBar">
<div class="lightBlueBarTitle"> Grouping tracks
into sets and hierarchies</div>
</div>
<div class="borderGuard">
Depending on how closely related they are, tracks can be organized into one of three
hierarchical containers:
<ul>
<li>"<A href="#multiWig">multiWig</A>" container: when the tracks are
all in signal (wiggle or bigWig) format and it makes sense to overlay
them.<br>
Example: a set of bigWig tracks with H3K27ac signal, all on the same
scale</li>
<li>"<A href="#compositeTrack">composite</A>" container: when the
tracks are expected to be configured together or have an internal
subgrouping, like cell type or cell treatment.<br>
Example: a set of ChIP-bigBeds in three different cell types</li>
<li>"<A href="#superTrack">superTrack</A>" container: when the tracks
share no specific configuration and you mostly want to show them
together.<br>
Example: a set of composite tracks or a mix of bigBed,
bigWig and bam</li>
</ul>
<A name="group"></A>
<A name="superTrack"></A>
<TABLE class="settingsTable" id="superTrack_-_Folder_Track_Settings">
<THEAD><TR><TD><DIV ID="superTrack_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
Supertrack (Folders) settings
</TH></TR>
<TR VALIGN=TOP><TD class="superTrack"><IMG class='toggle detail'>
<div class="format"><code class="level-base">superTrack on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="parent_supertrack">
<A name="parent_supertrack"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">parent <superTrack></code></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="superTrack_example">
<IMG class='toggle detail'>
<div class="format"><B>Example of a Supertrack</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="compositeTrack"></A>
<TABLE class="settingsTable" id="Composite_Track_Settings">
<THEAD><TR><TD><DIV ID="compositeTrack_hub_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'> Composite track settings</TH></TR>
<TR VALIGN=TOP><TD class="parent"><A name="parent"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">parent <composite> [off/on]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="compositeTrack"><IMG class='toggle detail'>
<div class="format"><code class="level-base">compositeTrack on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="allButtonPair"><A name="allButtonPair"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">allButtonPair on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="centerLabelsDense">
<A name="centerLabelsDense"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">centerLabelsDense <off/on></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="dragAndDrop"><A name="dragAndDrop"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">dragAndDrop subTracks</code></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="compositeTrack_example">
<IMG class='toggle detail'>
<div class="format"><B>Example of a Composite track</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="subGroups"></A>
<TABLE class="settingsTable" id="Composite_-_Subgroups_Settings">
<THEAD><TR><TD><DIV ID="subGroups_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
Composite track subgroup settings</TH></TR>
<TR VALIGN=TOP><TD class="subGroupN">
<A name="subGroupN"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-base">subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a>
[mTag1b=mTitle1b…]</code><BR>
<code class="level-base">subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a>
[mTag2b=mTitle2b…]</code><BR>
<code class="level-base">subGroup3</code>
<code class="level-base">subGroup4</code>
<code class="level-base">subGroup5</code>
<code class="level-base">subGroup6</code>
<code class="level-base">subGroup7</code>
<code class="level-base">subGroup8</code>
<code class="level-base">subGroup9</code>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="subGroups"><IMG class='toggle detail'>
<div class="format">
<code class="level-base">subGroups <gTag1=mTag1?> [gTag2= mTag2?]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="dimensions"><A name="dimensions"></A><IMG class='toggle detail'>
<div class="format"><code class="level-base">dimensions <dimX=gTag#>
[dimY=gTag#] [dimA=gTag# ...]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="filterComposite">
<A name="filterComposite"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">filterComposite <dim[A/B/C][=one]>
[dimB dimC ...]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="dimensionAchecked">
<A name="dimensionAchecked"></A><IMG class='toggle detail'>
<div class="format">
<code class="level-full">dimensionAchecked <mTag1a> [mTag1b …]</code><BR>
<code class="level-full">dimensionBchecked</code>
<code class="level-full">dimensionCchecked</code>
</div>
</TD></TR>
<TR VALIGN=TOP><TD class="sortOrder"><A name="sortOrder"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">sortOrder <gTag#=+/-> [gTag#=- …]</code></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="subGroups_hub_example">
<IMG class='toggle detail'>
<div class="format"><B>Examples of Composite tracks with Subgroups</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="view"></A>
<TABLE class="settingsTable" id="Composite_-_Views_Settings">
<THEAD><TR><TD><DIV ID="view_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
Composite track View settings
</TH></TR>
<TR VALIGN=TOP><TD class="view"><IMG class='toggle detail'>
<div class="format">
<code class='level-base'>subGroup1 view <Views> <vTag1a=vTitle1a>
[vTag1b=vTitle1b…]</code><BR>
<code class='level-required'>track <viewName></code><BR>
<span class="view"><code class="level-full">view <viewTag></code></span></div>
</TD></TR>
<TR VALIGN=TOP><TD class="parent_view"><A name="parent_view"></A><IMG class='toggle detail'>
<div class="format">
<code>subGroups view=<vTag1>…</code><BR>
<code>parent <viewName> [off/on]</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="viewUi"><A name="viewUi"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">viewUi on</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="configurable"><A name="configurable"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">configurable <off/on></code></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="view_example"><IMG class='toggle detail'>
<div class="format"><B>Example of a Composite track with Views</B></div>
</TD></TR>
</TABLE>
<BR><BR>
<A name="container"><A name="aggregate"><A name="multiWig"></A>
<TABLE class="settingsTable" id="Aggregate_or_Overlay_Track_Settings">
<THEAD><TR><TD><DIV ID="container_intro" class="intro"></DIV></TD></TR></THEAD>
<TR VALIGN=TOP><TH><IMG class='toggle oneSection'>
Aggregate or Overlay track settings
</TH></TR>
<TR VALIGN=TOP><TD class="container"><IMG class='toggle detail'>
<div class="format"><code class="level-full">container multiWig</code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="parent_container">
<A name="parent_container"></A><IMG class='toggle detail'>
<div class="format"><code>parent <containerTrack></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="aggregate"><IMG class='toggle detail'>
<div class="format"><code class="level-full">aggregate <transparentOverlay/stacked/solidOverlay/none></code></div>
</TD></TR>
<TR VALIGN=TOP><TD class="showSubtrackColorOnUi">
<A name="showSubtrackColorOnUi"></A><IMG class='toggle detail'>
<div class="format"><code class="level-full">showSubtrackColorOnUi on</code></div>
</TD></TR>
<TR class="examples" VALIGN=TOP><TD class="container_hub_example">
<IMG class='toggle detail'>
<div class="format"><B>Example of an Aggregate track</B></div>
</TD></TR>
</TABLE>
</div></div>
<!-- Deprecated settings -->
<div class="contentBorder">
<div class="borderGuard">
<A name="Deprecated"></A>
<H3>Miscellaneous Deprecated Settings</H3>
<TABLE class="settingsTable" id="Miscellaneous_Deprecated_Settings">
<TR VALIGN=TOP><TH WIDTH=100>Setting</TH><TH WIDTH=100>For Types</TH><TH>Notes</TH></TR>
<TR VALIGN=TOP>
<TD class="metadata"><A name="metadata"></A><code class="level-deprecated">metadata</code>
</TD>
<TD>all</TD><TD></TD>
</TR>
<TR VALIGN=TOP>
<TD class="noInherit"><A name="noInherit"></A><code class="level-deprecated">noInherit</code></TD><TD>all</TD><TD></TD>
</TR>
<TR VALIGN=TOP>
<TD class="useScore"><A name="useScore"></A>
<code class="level-deprecated">useScore</code></TD>
<TD>bed, factorSource, bed5FloatScore, broadPeak</TD>
<TD>Replaced with <A onclick="return jumpTo(this);" HREF="#">spectrum</A>.</TD>
</TR>
</TABLE>
</div>
</div>
<!-- End of specs -->
</div>
<!-- Next section -->
<div class="contentBorder">
<div class="borderGuard">
<TABLE class="settingsTable" id="toc"></TABLE>
</div></div>
<!-- Plain text -->
<!-- QA (BL) suggested removing this (leaving code in for now)
<pre id="plainToc">
</pre>
</div>
-->
<!-- - - - - - - - Documentation Library gets filled here with setting DIVs - - - - - - - -->
<div id="library">
<!--#include virtual="trackDbLibrary.shtml" -->
</div>
</BODY></HTML>