0e4e0c0af65eea70f64edbc68348ce0972c4bbf4 braney Fri Aug 28 16:45:00 2026 -0700 Correct the track types listed for trackDb settings, and the hub settings list The "For Types" list in the trackDb docs was wrong for about sixty settings, so the docs named the wrong track types for settings that have always worked. Most named only the older type and left out its big* counterpart. The clearest case is the multiple-alignment family: a bigMaf track is drawn and configured by the same code as a wigMaf track, but only speciesOrder said so, while irows, itemFirstCharCase, speciesGroups, speciesCodonDefault, speciesDefaultOff, treeImage, pairwiseHeight and speciesUseFile all claimed wigMaf alone. The hapCluster settings said vcf and not vcfTabix. noScoreFilter said bed while its own example uses type bigBed 6 +. Six settings said "all" for something that only works on item tracks. Two documented settings do not exist. pslSequence describes a variable that was replaced by the baseColor family long before the setting was listed, and nothing has read either spelling since; it is removed. noStems is renamed to lollyNoStems, which is what the Browser actually reads. That one mattered: hubCheck builds its list of valid settings from trackDbHub.html, so it accepted the spelling that does nothing and rejected the one that works. Fourteen settings that work in hubs had no entry in the hub spec, so hubCheck reported them as unrecognized. They are listed now: chainColor, chainNormScoreAvailable, pairwiseHeight, barChartMatrixUrl, mouseOverFunction, intronGap, filterBy, baseColorTickColor, speciesGroups, speciesDefaultOff, speciesCodonDefault, itemFirstCharCase, irows, and canPack with configureByPopup and origAssembly. The last three, along with filterBy and baseColorTickColor, were marked "NOT FOR HUBS", which was wrong: the Browser reads them from a hub's trackDb the same way it reads them from ours. The type setting on the hub page listed every type the Browser knows, including ones that only work for tracks loaded into our own databases. It now shows only the types a hub can use. A hub-specific blurb for this already existed and had never been referenced. Three settings had no blurb at all, so the generated trackDbSettings.json never saw them: metadata, noInherit and useScore. Written, and the five hand-written copies in trackDbDoc.html that had drifted from the library are brought back into line. The library's header told the reader to always check their work in trackDbTestBlurbs.html, which was deleted in November 2025. It now points at "make settings" instead. That target regenerates trackDbSettings.yaml and .json, which are updated here, and its name map gains an entry so the hub-specific type blurb is still keyed as "type". refs #37908 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index 1a2a1a335da..1a245417ff4 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -1,27 +1,31 @@ <!-- trackDb documentation Library In order to reference trackDb type and setting descriptions in multiple documents, this library file is designed to hold the one definitive copy of the setting or type description. *** Go ahead and try your changes by following existing examples. If you have questions, read the detailed explanation below. *** Your changes can be seen in hgwdev or your sandbox when they are in: /usr/local/apache/htdocs-{sandbox}/goldenPath/help/trackDb/ A "make" should get them there. - ALWAYS VIEW trackDbTestBlurbs.html AFTER MODIFYING THIS FILE !!!!!!! + ALWAYS CHECK THIS FILE AFTER MODIFYING IT !!!!!!! + Run "make settings", which rebuilds trackDbSettings.yaml and .json from this + file and reports any blurb it could not read. Then view trackDbDoc.html and + trackDbHub.html and open the settings you touched. + (The old trackDbTestBlurbs.html test page was dropped in Nov 2025.) How to add/maintain this documentation: There are 2 essential parts to trackDb*.html DOCS: I) this LIBRARY and II) the HTML PAGES. I) This LIBRARY consists of DIVs that contain "blurbs" describing settings and types. Example: <DIV class="someSetting"><span class="types bed bigBed"></span> <div class="format"><code>someSetting <minVal></code></div> <P>Both <code>bed</code> and <code>bigBed</code> type tracks use <code>someSetting</code> in combination with <A onclick="return jumpTo(this);" HREF="#">visibility</A> to accomplish something.</P> <P><B>Example:</B></P> <pre> someSetting 100</pre> </DIV> - Each "blurb" DIV should have the class={setting}. There MUST be only one uniquely classed @@ -39,31 +43,33 @@ visibility setting can be accomplished as: <A onclick="return jumpTo(this);" HREF="#">visibility</A> which is identical to <A HREF="#visibility">visibility</A> - Any setting or code that is not made into a <A> link should be wrapped with <code> tags. - "Type setting blurbs" are the same as other setting blurbs except that there should be a separate "example blurb" DIV with class of type_example (e.g. <DIV class="bed_example">). This will allow a type definition to be followed by multiple type specific settings then be completed by the example that references those settings. - These example blurbs should also have a "class=format" DIV but in this case it contains a title to the example: <div class="format"><B>Examples of item base types</B></div>. - Exmples should make use of <PRE> tags and preferrably multiple real life examples. - Document introductions and section introductions may also be shared by multiple documents and therefore may be included here as "intro blurb" DIVs as: <DIV class="bed_intro">. - intro DIVs do not contain a class="format" DIV. - - Use trackDbTestBurbs.html to test blurbs you add or modify. It runs javascript tests. + - Run "make settings" to check a blurb you add or modify. trackDbSettingsGen.py + parses this file and names any blurb whose types span, format div or description + it could not read. HINT: It is the class={setting} that ties things togther. If there is a need for multiple descriptions of the same setting, then create multiple blurb DIVs with different classes as: <DIV class="parent"> and <DIV class="parent_view">. II) Document HTML PAGES should include this trackDbLibrary.html with server side includes and wrapped in <DIV ID="library"> tags. - Documents may differ, but using trackDbDoc.html as the example, the setting documentation is organized into tables by trackDb "type", so that settings are documented in the context of their use. The (usually) single cell rows contain the settings. The settings specification includes a <DIV> with a class attribute of value "format", and the setting name embedded in <CODE> tags. In the trackDbHub document, the <CODE> tag has a class whose value defines the support level for the setting, as 'class="level-*"', where '*' is one of the levels defined in the introduction of the trackDbHub document. Note: New settings should always be added to the current (highest version) trackDbHub document in this directory (e.g. trackDbHub.v2.html) and designated "level-new". @@ -193,51 +199,54 @@ supported are called out at the top of the Hub Track Database Definition page. In many cases the type setting includes additional parameters to further specify the data format. Some track types have additional setting requirements, to be discussed below.</P> <P><B>Example:</B> </P> <pre> type bed 6 +</pre> </DIV> <DIV class="type_for_hubs"><span class="types all"></span> <div class="format"><code>type</code></div> <P class="isRequired">Required: <span class="red">Yes</span></P> <P>Declares the format of the data and is used to determine display methods and options.</P> - <P>Valid settings:</P> + <P>Valid settings for a hub:</P> <P> <A onclick="return jumpTo(this);" HREF="#">bam/cram</A>, <A onclick="return jumpTo(this);" HREF="#">bigBarChart</A>, <A onclick="return jumpTo(this);" HREF="#">bigBed</A>, <A onclick="return jumpTo(this);" HREF="#">bigChain</A>, + <A onclick="return jumpTo(this);" HREF="#">bigGenePred</A>, <A onclick="return jumpTo(this);" HREF="#">bigInteract</A>, <A onclick="return jumpTo(this);" HREF="#">bigLolly</A>, <A onclick="return jumpTo(this);" HREF="#">bigMaf</A>, + <A onclick="return jumpTo(this);" HREF="#">bigNarrowPeak</A>, <A onclick="return jumpTo(this);" HREF="#">bigPsl</A>, <A onclick="return jumpTo(this);" HREF="#">bigWig</A>, <A onclick="return jumpTo(this);" HREF="#">halSnake</A>, <A onclick="return jumpTo(this);" HREF="#">hic</A>, <A onclick="return jumpTo(this);" HREF="#">vcfTabix</A>, + <A onclick="return jumpTo(this);" HREF="#">vcfPhasedTrio</A>. + </P> <P>Detailed descriptions of each type can be found below. In many cases the type setting includes additional parameters to further specify the data format. Some track types have additional setting requirements, to be discussed below.</P> - <P><B>Example:</B> - </P> + <P><B>Example:</B></P> <pre> type bigBed 6 +</pre> </DIV> <DIV class="shortLabel"><span class="types all"></span> <div class="format"><code>shortLabel</code></div> <P class="isRequired">Required: <span class="red">Yes</span></P> <P>Specifies the track's "short label", which is used in a number of places in the Browser to identify the track. For example, the short label is displayed alongside the track in the Browser image. This label must be brief and is limited to 17 printable characters. Some <a href="../../../FAQ/FAQcustom.html#custom13">special characters</a> are allowed in the shortLabel.</P> <P><B>Example:</B> </P> <pre> shortLabel Human mRNAs</pre> @@ -257,30 +266,46 @@ <P><B>Example:</B></P> <pre> longLabel Human mRNAs from GenBank</pre> </DIV> <DIV class="meta"><span class="types all"></span> <div class="format"><code>meta</code></div> <P class="isRequired">Required: No</P> <P> Meta specifies the metadata tag for this track. This tag is a key into the metadata table specified in either metaDb or metaTab in the genomes.txt file. The meta tag can be any alphanumeric string. Each meta tag should appear in a trackDb stanza AND in either the tab-separated file specified by metaTab, or tagStorm file specified by metaDb in the hub's genomes.txt file. Examples on how to include metadata in your hubs can be found on the following <a href="/goldenPath/help/metadata.html">metadata guide</a>. </DIV> +<DIV class="metadata"><span class="types all"></span> +<div class="format"><code>metadata <name=value> [<name=value> ...]</code></div> + <P><I>Deprecated. Use <A onclick="return jumpTo(this);" HREF="#">meta</A> instead.</I></P> + <P>Attaches metadata to a track as a list of <code>name=value</code> pairs on one line. + Wrap a value that contains spaces in double quotes. A word starting with <code>#</code> + ends the line, so anything after it is a comment. The pairs are shown on the track + description page and on the item details page.</P> + <P>The <code>meta</code> setting replaces this one. It keeps the metadata in a single + file for the whole hub, named by <code>metaDb</code> or <code>metaTab</code> in + <code>genomes.txt</code>, instead of repeating it in every stanza. See the + <a href="/goldenPath/help/metadata.html">metadata guide</a>. The Browser still reads + <code>metadata</code>, but <code>meta</code> wins when a stanza has both.</P> + <P><B>Example:</B></P> + <pre> metadata cellType=K562 antibody=CTCF lab="Broad Institute"</pre> +</DIV> + <DIV class="visibility"><span class="types all"></span> <div class="format"><code>visibility</code></div> <P class="isRequired">Required: No</P> <P>Visibility (i.e. "display mode") specifies which of 5 modes (including 'hide') should be used to display the track within the Browser image. This setting is almost always dynamically customizable by each user. The exact configuration of the display for each mode depends upon the track's type, and some modes may not be supported for certain track types. Please note visibility settings in composite subtracks are directly inherited from the parent. Therefore, any visibility lines added at the subtrack level of a composite will be ignored. The one exception is a <A HREF="#faceted_composite">faceted composite</A>, where the parent's visibility is a maximum rather than a value the subtracks inherit, and subtrack visibility lines are honored up to that maximum. Be sure to experiment with this setting to verify that it works as expected for your track type and track structure.</P> <P>Valid settings:</P> @@ -406,33 +431,40 @@ </div> <BR> </DIV> <DIV class="linkDataUrl"><span class="types bigChain "></span> <div class="format"><code>linkDataUrl <url/relativePath></code></div> <P class="isRequired">Required: <span class="red">For Hubs</span></P> <P>The location of a remote data file containing the chain link data.</P> </DIV> <DIV class="lollyField"><span class="types bigLolly"></span> <div class="format"><code>lollyField <integer></code></div> Use the given field as the height of the lollipop. </DIV> -<DIV class="noStems"><span class="types bigLolly"></span> -<div class="format"><code>noStems <on/off></code></div> - Don't draw the stems of the lollipops. +<DIV class="lollyNoStems"><span class="types bigLolly"></span> +<div class="format"><code>lollyNoStems <on/off></code></div> + <P>Draw the lollipop heads without the stems that normally connect them to + the baseline.</P> + <P>This setting was documented as <code>noStems</code> until August 2026. + That spelling never worked, because the Browser has always read + <code>lollyNoStems</code>. A track using <code>noStems</code> draws its + stems as usual.</P> + <P><B>Example:</B></P> + <pre> lollyNoStems on</pre> </DIV> <DIV class="lollySizeField"><span class="types bigLolly"></span> <div class="format"><code>lollySizeField <integer></code></div> Use the given field as the size of the lollipop, measured in percentage of the total available drawing area. </DIV> <DIV class="lollyMaxSize"><span class="types bigLolly"></span> <div class="format"><code>lollyMaxSize <integer></code></div> The maximum size of a lollipop in the file, used to establish margins. </DIV> <DIV class="yAxisLabel"><span class="types bigLolly"></span> <div class="format"><code>yAxisLabel.<integer> <integer> <on/off> <R,G,B> <string> </code></div> Add a label on the y axis at the given position. Draw a line of color if requested. @@ -485,31 +517,32 @@ <DIV class="boxedCfg"><span class="types all"></span> <div class="format"><code>boxedCfg <on/off></code></div> <!-- <P><I>NOT FOR HUBS</I></P> says Jim, but why not. Already used. --> <P>Configuration controls can be placed inside a box on the configuration page. This setting is decorative only, but can make a busy page look more cohesive. Not all track types currently support this feature, but the most common types do, including wig, bigWig, bed, and bigBed. DEFAULT: off.</P> <P><B>Example:</B></P> <pre> boxedCfg on</pre> </DIV> <DIV class="canPack"><span class="types all"></span> <div class="format"><code>canPack <off/on></code></div> - <P><I>NOT FOR HUBS. Deprecated.</I></P> + <P><I>Deprecated. The track type usually implies whether pack and + squish are offered, so this setting is rarely needed.</I></P> <P>Most tracks can be displayed in all five visibilities modes. However on some track types such as wiggles, the <code>squish</code> and <code>pack</code> modes offer no real advantage over the <code>dense</code> and <code>full</code> modes. By default, these tracks will not offer the <code>squish</code> and <code>pack</code> vilibility settings. Nevertheless, you can make your track offer these visibility choices by turning canPack on. Note: subtracks of composites will always offer all five choices.</P> <P><B>Example:</B></P> <pre> canPack on</pre> </DIV> <DIV class="color"><span class="types all"></span> <div class="format"><code>color <red,green,blue></code></div> <P>Many track types allow the color of the data displayed in the image to be specified with @@ -540,31 +573,30 @@ </DIV> <DIV class="chromosomes"><span class="types all"></span> <div class="format"><code>chromosomes <chr1,chr2,...></code></div> <P>Some datasets do not contain data for all chromosomes of a genome. When this is true, use this setting as a comma-separated list of the chromosomes that are covered. The system displays a message that no data is available when the user browses chromosomes not included in this list.</P> <P><B>Example:</B></P> <pre> chromosomes chr1,chr7,chr18,chr19,chr22,chrX,chrM</pre> </DIV> <DIV class="configureByPopup"><span class="types all"></span> <div class="format"><code>configureByPopup <on/off></code></div> - <P><I>NOT FOR HUBS.</I></P> <P>Most track displays that can be configured by a user can also be configured from directly within the Browser image through a right-click option that pops up a configuration dialog. While this functionality works on the majority of track types, some configuration dialogs are too complex or have too much embedded javascript control to be reliably configured through a pop-up. To turn off the ability to configure the track via right-click, change this setting to "off". The user will still be able to configure the track on the track's configuration page. DEFAULT: on.</P> <P><B>Example:</B></P> <pre> configureByPopup off</pre> </DIV> <DIV class="darkerLabels"><span class="types all"></span> <div class="format"> @@ -740,31 +772,30 @@ <P><B>Example:</B></P> <pre> otherDb mm10</pre> <P>This example sets the second assembly in the alignment to the mouse mm10 assembly.</P> </DIV> <DIV class="otherTwoBitUrl"><span class="types chain bigChain psl bigPsl"></span> <div class="format"><code>otherTwoBitUrl <url/relativePath></code></div> <P>For pairwise alignment tracks this can specify where to find the query sequence This setting can be used in psl, bigPsl, chain, and bigChain tracks.</P> <P><B>Example:</B></P> <pre> otherTwoBitUrl https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit</pre> </DIV> <DIV class="origAssembly"><span class="types all"></span> <div class="format"><code>origAssembly <db></code></div> - <P><I>NOT FOR HUBS.</I></P> <P>The original assembly version for which the dataset was generated. Datasets generated by mapping to one genome assembly may prove useful enough to map to a more recent assembly. Ideally datasets will be regenerated to map to the new assemblies coordinates, but sometimes this is not practical or expedient. Therefore, the dataset may have its genome coordinates "lifted over" to the more recent assembly. In some cases this results in an inferior but nevertheless useful representation. Such datasets should have their original assembly defined with this setting.</P> <P><B>Example: </B> </P> <pre> origAssembly hg18</pre> </DIV> @@ -1304,38 +1335,30 @@ <code>type broadPeak</code><BR> <code>type coloredExon</code><BR> <code>type gvf</code><BR> <code>type ld2</code><BR> <code>type narrowPeak</code><BR> <code>type peptideMapping</code></div> <P>Each of these is a specialized variation of the bed format. Their specialized definitions should be sought elsewhere. However, these item tracks share many of the same configuration options available to bed tracks.</P> <!--DONNA - rewrite above --> <P><em>An example can be found below.</em></P> </DIV> -<DIV class="bigDataUrl2"><span class="types bigBed bigWig bam vcfTabix"></span> -<div class="format"> - <code>bigDataUrl2 <url/relativePath></code></div> - <P>This setting is for remote data file type - tracks (e.g. bigWig) and is fully described in the "<A HREF="#bigDataUrl">Common - trackDb settings</A>" portion of this document.</P> -</DIV> - <DIV class="colorByStrand"><span class="types bed bigBed"></span> <div class="format"><code>colorByStrand <red,green,blue> <red,green,blue></code></div> <P>To color items differently by the strand they align to, use the colorByStrand setting. The first color will be used for plus strand alignments and the second for the minus strand. This setting is incompatible with <code>spectrum</code> and all items on the same strand will have the same color, regardless of the item's <code>score</code>.</P> <P><B>Example:</B></P> <pre> colorByStrand 255,0,0 0,0,255</pre> <P>Plus strand alignments will be colored red, and minus strand alignments will be blue. This setting is incompatible with <code>spectrum</code>, and therefore all items on the same strand will have the same color, regardless of the item's <code>score</score>.</P> </DIV> @@ -1439,53 +1462,53 @@ space for 4 characters, no label is drawn at all. If there is more space, the label is drawn with a contrasting color onto the exon-like blocks. If they are too short for the text, it is trimmed to fit into the available space and the suffix "..." appended. Note that features should not have too long thin (UTR) regions, as the text might be hard to read in these parts.<br> To keep the text readable, the arrows that indicate the strand are shown over introns, but suppressed on blocks, so the statement should be used for tracks where strand is not of primary importance, not defined in the BED strand field or deactivated with <A onclick="jumpTo(this)" HREF="#">exonArrows</A>. </P> <P><B>Example:</B></P> <pre> labelOnFeature on</pre> </DIV> -<DIV class="exonArrows"><span class="types genePred bed broadPeak"></span> +<DIV class="exonArrows"><span class="types bed bigBed genePred bigGenePred psl bigPsl chain bigChain narrowPeak bigNarrowPeak broadPeak"></span> <div class="format"><code>exonArrows <on/off></code></div> <P>On tracks that show exons or blocks within features, exon arrows allow the user to jump to the next exon or block outside the image. Exon arrows are typically shown by default in these types of tracks, with the exception of tracks in the Regulation group. The arrows can be explicitly shown or hidden using this setting. </P> <P><B>Example:</B></P> <pre> exonArrows off</pre> </DIV> -<DIV class="exonNumbers"><span class="types genePred bed psl bigBed bigGenePred"></span> +<DIV class="exonNumbers"><span class="types genePred bigGenePred bed bigBed psl bigPsl"></span> <div class="format"><code>exonNumbers <on/off></code></div> <P>A mouseover that shows the exon and intron numbers can be explicitly shown or hidden using this setting. The default is "on" for the track types genePred and bigGenePred.</P> <P><B>Example:</B></P> <pre> exonNumbers off</pre> <P>The text can be set with the options "exonText" and "intronText". It defaults to "exon" and "intron", respectively.</P> </DIV> -<DIV class="Filter"><span class="types bed narrowPeak broadPeak"></span> +<DIV class="Filter"><span class="types bed bigBed narrowPeak bigNarrowPeak broadPeak"></span> <div class="format"> <code><column>Filter <low>[:<high>]</code><BR> <code>scoreFilter <low>[:<high>]</code><BR> <code>pValueFilter</code><BR> <code>qValueFilter</code><BR> <code>signalFilter</code><BR> <code><column>FilterLimits <low>[:<high>]</code><BR> <code><column>FilterByRange <off/on></code> </div> <P>A number of numerical filters are available for bed tracks. These are conveniently named by the field that is filtered on. The most common numerical filter is based on the standard bed field <code>score</code>, and is thus controlled by the <code>scoreFilter</code> setting. Other examples are pValueFilter, qValueFilter and @@ -1549,35 +1572,33 @@ can be replaced with <code>filter.score 400</code> and <code>filterByRange.score 0:1000</code>. The advantage of switching to the filter.<fieldName> approach is that filters can also be added on additional bigBed <fieldNames> such as filterText.disease or filterValues.cellType where bigBeds defined with a disease or cellType column can be filtered. See filter.<fieldName> for more information and examples. </p> <P><B>Example:</B></P> <pre> scoreFilter 300 scoreFilterLimits 200:1000</pre> <P>The standard bed field of <code>score</code>, which is an integer will be used to filter items in the track. By default, items with scores below 300 will be excluded. The filter cannot be set to less than 200 or more than 1000..</P> </DIV> -<DIV class="filterBy"><span class="types bed bigBed genePred psl factorSource"></span> +<DIV class="filterBy"><span class="types bed bigBed genePred bigGenePred psl bigPsl bigLolly factorSource"></span> <div class="format"><code>filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]</code></div> - <!-- DONNA -- redo --> - <P><I>NOT FOR HUBS. Not yet supported by bigBeds</I></P> <P>Another method of filtering items relies upon discrete values. One or more fields such as <code>name</code> or <code>score</code> may contain a limited number of discrete values that can be filtered on. These discrete values will be displayed in a dropdown list from which the user can choose one or more options. While the maximum number of options in the list is not limited, displaying too many options can be confusing for the user. </P> <P><I>Setting complexities:</I></P> <UL> <LI> Because filters for different fields are delimited by whitespace, any whitespace in titles and labels should be replaced by the '<code>_</code>' (underscore) character.</LI> <LI> Each field/option pair is joined by '<code>=</code>' (equal sign).</LI> <LI> The field portion @@ -2248,100 +2269,115 @@ exceeded, the track switches to coverage mode. Default: 1000. For <code>type bigBed</code> tracks, this setting can never be larger than the hg.conf setting bigBedMaxItems, which by default is 100,000 at UCSC. </P> <P>bigBedMaxItems is configured globally for a Genome Browser server and sets an upper limit on how many features can be loaded at most from a bigBed file, to avoid a single track making a Genome Browser view unusable at high zoom levels so it the upper limit for all maxItems settings of any tracks shown on a Genome Browser. If you have feedback on these values, please do not hesitate to contact us.</P> <P><B>Example:</B> </P> <pre> maxItems 25</pre> </DIV> -<DIV class="maxWindowCoverage"><span class="types bed genePred bam rmsk narrowPeak broadPeak bigWig bedLogR"></span> +<DIV class="maxWindowCoverage"><span class="types bed bigBed genePred bigGenePred psl bigPsl chain bigChain narrowPeak bigNarrowPeak broadPeak bam rmsk bedLogR vcf vcfTabix"></span> <div class="format"><code>maxWindowCoverage <integer></code></div> <p>When too many individual bed items might be shown in the Browser image (such as might occur when a large region of a chromosome is viewed), <code>maxWindowCoverage</code> will switch the track into density coverage plot when the window contains more than the specified number of bases.</p> <P><B>Example:</B></P> <pre> maxWindowCoverage 10000000</pre> <p>Browser images that show more than 10,000,000 bases will result in the track data being displayed as a density coverage graph.</p> </DIV> -<DIV class="maxWindowToDraw"><span class="types bed genePred bam rmsk narrowPeak broadPeak bigWig bedLogR"></span> +<DIV class="maxWindowToDraw"><span class="types all"></span> <div class="format"><code>maxWindowToDraw <integer></code></div> <p>When too many individual bed items might be shown in the Browser image (such as might occur when a large region of a chromosome is viewed), <code>maxWindowToDraw</code> will trigger a choice to display a message asking users to zoom in to a smaller region.</p> <p>Depending on the current visibility of the bed track and which other tracks are being shown concurrently, the Browser may automatically reduce the display to pack or dense mode in some cases. The <code>maxWindowToDraw</code> setting allows you to force users to zoom in as an overriding message will block out the data display. Unlike the <code>maxItems</code> setting, which controls the display of vertical space and forces a display to dense when the maximum number of items is exceeded, the <code>maxWindowToDraw</code> setting dictates the number of bases to be displayed in a window before the track is obscured with a message explaining the requirement for zooming-in. Even without this setting, there are browser operations that will ultimately prevent too many items from being displayed by forcing a visualized summary in dense mode as noted.</p> <P><B>Example:</B></P> <pre> maxWindowToDraw 10000000</pre> <p>Browser images that show more than 10,000,000 bases will result in the track data being obscured with a note across the genomic range stating the message <code>zoom in to <= 10,000,000 bases to view items</code>.</p> </DIV> -<DIV class="minGrayLevel"><span class="types bed broadPeak narrowPeak bedLogR bigBed"></span> +<DIV class="minGrayLevel"><span class="types bed bigBed broadPeak narrowPeak bigNarrowPeak bedLogR bigInteract"></span> <div class="format"><code>minGrayLevel <1-9></code></div> <P>When a bed track contains the standard field <code>score</code>, and when that score is used to present items in gray or color scale (see <A onclick="jumpTo(this)" HREF="#">spectrum</A>), this setting specifies the lightest shade to be used. This prevents the lowest scores from being displayed in too light of a color to easily view. Set the value in the range 1 - 9, lightest to darkest.</P> <P><B>Example:</B></P> <pre> minGrayLevel 4</pre> <P>This sets the lowest scores to slightly less than medium gray, while the highest scores appear black.</P> </DIV> -<DIV class="noScoreFilter"><span class="types bed bedGraph bedLogR gvf"></span> +<DIV class="noScoreFilter"><span class="types bed bigBed bedGraph bedLogR gvf"></span> <div class="format"><code>noScoreFilter on</code></div> <P>By default, bed tracks with 5 or more standard bed fields that contain either a '<code>.</code>' or a '<code>+</code>' in the type setting will be filterable on <code>score</code>; that is, they will have an assumed setting of "<code>scoreFilter 0</code>". To turn this old-style default off, include the "<code>noScoreFilter</code>" setting.</P> <!-- DONNA -- what should they use instead? TIM ANSWERS: The implicit score filtering bases upon '.' or '+' is confusing and not used by other item based tracks. Ideally, score filtering is specifically requested by "scoreFilter #", which would make "noScoreFilter on" the unneeded default. -- --> <P><B>Example:</B></P> <pre> type bigBed 6 + noScoreFilter on </pre> </DIV> -<DIV class="spectrum"><span class="types all"></span> +<DIV class="useScore"><span class="types bed bigBed bigGenePred psl bigPsl"></span> +<div class="format"><code>useScore 1</code></div> + <P><I>Deprecated. Use <A onclick="return jumpTo(this);" HREF="#">spectrum</A> instead.</I></P> + <P>Shades each item by its <code>score</code> field, so low scores draw in light gray and + high scores draw near black. <code>spectrum on</code> does the same thing and is the + spelling to use in a new track. The Browser treats the two names as one setting, and + <code>scoreMin</code>, <code>scoreMax</code> and + <A onclick="return jumpTo(this);" HREF="#">minGrayLevel</A> tune both the same way.</P> + <P>In a trackDb file or a hub, any value turns the shading on, including + <code>useScore 0</code>, because the Browser only checks whether the setting is present. + In a custom track the value is read, and <code>0</code> turns the shading off.</P> + <P><B>Example:</B></P> + <pre> useScore 1</pre> +</DIV> + +<DIV class="spectrum"><span class="types bed bigBed bigGenePred psl bigPsl"></span> <div class="format"> <code>spectrum on</code><BR> <code>scoreMax <integer></code><BR> <code>scoreMin <integer></code></div> <P>Replaces <code>useScore</code>.</P> <P>If your track is a <code>bed 5</code> or greater, then the standard bed <code>score</code> field exists. This score, which is expected to vary from 0-1000, can be used to control the shading of bed items drawn in the Browser image. To activate this feature, set <code>spectrum on</code>. Lower scores will be shaded in light gray by default, while higher scores will trend towards black. This can be modified in a number of ways:</P> <UL> <!-- The below statement about color and altColor is not accurate and removed 1/4/17 <LI> <code><A onclick="jumpTo(this)" HREF="#">color</A></code> @@ -2514,31 +2550,31 @@ </P> <p> bigBed files are often created using the UCSC <tt>bedToBigBed</tt> program. By default, this program expects only a single word for BED item names. To tell the program to accept multiple words separated by spaces (required for this track setting), you will need to use the <tt>-tab</tt> option for <tt>bedToBigBed</tt>. This tells the program that that tab characters are used instead of spaces to separate fields of the BED file. Please note that this option will only work if tab characters are used as the field separator throughout your BED file. More information on creating bigBed files is available on our <a href="../bigBed.html">bigBed Track Format</a> page. </p> </DIV> -<DIV class="baseColorUseSequence"><span class="types all"></span> +<DIV class="baseColorUseSequence"><span class="types bed bigBed genePred psl bigPsl chain bigChain bam"></span> <div class="format"><code>baseColorUseSequence <extFile {seqTable} / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit ></code></div> <!-- DONNA -- redo --> <P>Specifies where item sequence can be found (if any) so that item sequence, or differences from genomic sequence, can be drawn when viewing a sufficiently small region. </P> <UL> <LI>If <code>extFile</code> is specified, two additional parameters are required, the name of the seq table followed by the name of the extFile table to use in looking up the sequence. These tables are loaded by hgLoadSeq. </LI> <LI>If @@ -2550,123 +2586,138 @@ <LI>If <code>nameIsSequence</code> is specified then the 4th column (<code>name</code> or <code>sequence</code>) contains the sequence. (see hg/lib/encode/tagAlign.as)</LI> <LI>If <code>seq1Seq2</code> is specified then the 7th & 8th columns (<code>seq1</code> and <code>seq2</code>) contain the left and right pairs of the sequence. (see hg/lib/encode/pairedTagAlign.as)</LI> <LI>If <code>ss</code> is specified then a user-provided blat sequence is looked for.</LI> <LI>If <code>2bit</code> is specified then looks for sequence in the file specified by the <code>otherTwoBitUrl</code> tag. </UL> </DIV> -<DIV class="baseColorUseCds"><span class="types bed genePred psl bigPsl"></span> +<DIV class="baseColorUseCds"><span class="types bed bigBed genePred bigGenePred psl bigPsl"></span> <div class="format"><code>baseColorUseCds <given></code></div> <P>Specifies where coding sequence (CDS) coordinates can be found (if any) so that codons can be drawn when viewing a sufficiently small region.</P> <P><B>Example:</B></P> <pre> baseColorUseCds given</pre> </DIV> -<DIV class="baseColorDefault"><span class="types all"></span> +<DIV class="baseColorDefault"><span class="types bed bigBed genePred bigGenePred psl bigPsl chain bigChain bam"></span> <div class="format"><code>baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> <P>Specifies the default drawing mode. The <code>itemBases</code>, <code>itemCodons</code>, <code>diffBases</code> and <code>diffCodons</code> options are applicable only if the track has sequence, as specified by the <code>baseColorUseSequence</code> setting. The <code>genomicCodons</code>, <code>itemCodons</code> and <code>diffCodons</code> are applicable only if the track has CDS info, as specified by the <code>baseColorUseCds</code> setting.</P> </DIV> -<DIV class="baseColorTickColor"><span class="types bed bigBed"></span> +<DIV class="baseColorTickColor"><span class="types bed bigBed psl bigPsl"></span> <div class="format"><code>baseColorTickColor <lighterShade/contrastingColor></code></div> - <P><I>NOT FOR HUBS. Not yet supported by bigBeds</I></P> - <P>Choose a <code>contrastingColor</code> (this is often - white) or <code>lighterShade</code> of color. This should be the - same color as would be chosen for the base text if the user were - zoomed in to base level.</P> + <P>Sets the color of the tick marks that mark where item bases differ from the + genome. Those marks appear when the track draws with + <code>baseColorDefault diffBases</code> and the view is zoomed out past base + level. Their default color is red.</P> + <UL> + <LI><code>contrastingColor</code>: a color that stands out against the item + color, often white.</LI> + <LI><code>lighterShade</code>: a lighter version of the item color.</LI> + </UL> + <P>Both values are worked out from the item's own color, so this setting does + nothing unless the track gives each item a color. In a hub the way to do that is + <A onclick="return jumpTo(this);" HREF="#">colorByStrand</A>. Without it the + setting is read and ignored, and the tick marks stay red. + <code>itemRgb</code> does not count here: it colors an item as it is drawn, but + it does not give the track the per-item color this setting reads.</P> + <P><B>Example:</B></P> + <pre> + colorByStrand 0,0,200 200,0,0 + baseColorDefault diffBases + baseColorTickColor contrastingColor</pre> </DIV> -<DIV class="showDiffBasesAllScales"><span class="types all"></span> +<DIV class="showDiffBasesAllScales"><span class="types bed bigBed genePred psl bigPsl chain bigChain bam"></span> <div class="format"><code>showDiffBasesAllScales on</code></div> <P>Show base differences for all zoom levels.</P> <!-- DONNA -- how do you show the differences? --> </DIV> -<DIV class="showDiffBasesMaxZoom"><span class="types all"></span> +<DIV class="showDiffBasesMaxZoom"><span class="types bed bigBed genePred psl bigPsl chain bigChain bam"></span> <div class="format"><code>showDiffBasesMaxZoom <basesPerPixel></code></div> <P>Show annotations highlighting base or codon differences only if current zoom level does not exceed <code>basesPerPixel</code> (a float). <code>showDiffBasesAllScales</code> should also be set to make this useful.</P> </DIV> -<DIV class="showCdsAllScales"><span class="types psl"></span> +<DIV class="showCdsAllScales"><span class="types psl bigPsl"></span> <div class="format"><code>showCdsAllScales on</code></div> <P>Show CDS for PSL tracks at all zoom levels.</P> </DIV> -<DIV class="showCdsMaxZoom"><span class="types psl"></span> +<DIV class="showCdsMaxZoom"><span class="types psl bigPsl"></span> <div class="format"><code>showCdsMaxZoom <basesPerPixel></code></div> <P>Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS for psl tracks. In conjunction with this setting, <code>showCdsAllScales</code> must be set on and <code>showDiffBasesMaxZoom</code> should be set to a value not more than <code>showCdsMaxZoom</code> to make this display configuration useful.</P> <P><hr class="example" /><B>Examples:</B></P> <pre> baseColorDefault genomicCodons baseColorUseCds given showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 baseColorUseCds table hgFixed.transMapGeneUcscGenes baseColorUseSequence lfExtra baseColorDefault diffCodons baseColorTickColor lighterShade showDiffBasesAllScales . showCdsAllScales . </pre> <!-- DONNA -- redo <P><I>TODO: Explain examples, expand option explanation</I></P> DONNA -- finish --> </DIV> -<DIV class="exonArrowsDense"><span class="types bed"></span> +<DIV class="exonArrowsDense"><span class="types bed bigBed genePred bigGenePred psl bigPsl chain bigChain narrowPeak bigNarrowPeak broadPeak bam"></span> <div class="format"><code>exonArrowsDense <off/on></code></div> <P>On tracks that show exons or blocks within items, exon arrows allow the user to jump to the next exon/block outside the image. Use this setting to display exon arrows even when the track is in dense mode.</P> </DIV> <DIV class="itemDetailsHtmlTable"><span class="types bed genePred psl"></span> <div class="format"><code>itemDetailsHtmlTable <table></code></div> <P><I>NOT FOR HUBS. Supplemental table must be in local database.</I></P> <P>Use this setting to specify a table, indexed by item name, that contains an optional HTML fragment to display on the details page for this item. The expected columns in the table are "name" and "html".</P> <P><B>Example</B>:</P> <pre> itemDetailsHtmlTable pseudoGeneDetails</pre> </DIV> -<DIV class="itemImagePath"><span class="types bed"></span> +<DIV class="itemImagePath"><span class="types bed bigBed"></span> <div class="format"><code>itemImagePath <path> <suffix></code><BR> <code>itemBigImagePath <path> <suffix></code></div> <!-- <P><I>Not found in any of the Genome Browser trackDb.ra files. Custom or dataHub setting.</I></P> --> <P>Items can be associated with images and the images can be made visible with these two settings. The <code>itemImagepath</code> specifies a URL path to a directory with image files named in the format <code>{name}.{suffix}</code>. The name is retrieved from the table or remote data file. This image will be displayed on the item detaiIs page. If <code>itemBigImagePath</code> is also supplied, then a link to a larger image will be provided. If the path provided is local to the browser then the path should be relative.</P> <P><B>Example</B>:</P> <pre> @@ -2677,31 +2728,31 @@ the image <code>images/myTrackImages/fred.png</code> and will also provide a link to a larger image at <code>http://bigImages.com/myTrackImages/fred.jpg</code>.</P> </DIV> <DIV class="mafTrack"><span class="types bed"></span> <div class="format"><code>mafTrack <trackName></code></div> <P><I>NOT FOR HUBS</I></P> <P>By specifying a multiple alignments track, the item details page will illustrate the differences for that item across a number of species. </P> <P><B>Example:</B></P> <pre> mafTrack multiz46way</pre> </DIV> -<DIV class="nextExonText"><span class="types all"></span> +<DIV class="nextExonText"><span class="types bed bigBed genePred bigGenePred psl bigPsl chain bigChain narrowPeak bigNarrowPeak broadPeak"></span> <div class="format"> <code>nextExonText <str></code><BR> <code>prevExonText <str></code></div> <P>For tracks that offer multiple block items such as gene models, the next/previous exon arrows are usually displayed by default in the Browser. The functionality of these tiny arrows is described by mouse-over "tool tips" that default to "Next Exon" and "Prev Exon". If the blocks do not represent exons, you can adjust the tool tip text to the appropriate information with these two settings.</P> <P><B>Example:</B></P> <pre> nextExonText "Next Match" prevExonText "Previous Match" </pre> </DIV> @@ -2960,31 +3011,31 @@ </DIV> <DIV class="maxHeightPixels"><span class="types wig bigWig bedGraph bigInteract"></span> <div class="format"><code>maxHeightPixels <max:default:min></code></div> <P>The amount of vertical viewing space for your signal track should be declared, though it is configurable by the user. Typically it is set to no more than 100 pixels and no less than 8, with a default of 16 or 32 pixels.</P> <P><B>Example:</B></P> <pre> maxHeightPixels 100:16:8</pre> <P>The browser will display the track as 16 pixels high, but the user can scale it up to 100 pixels.</P> </DIV> -<DIV class="maxWindowToQuery"><span class="types bed bigWig bedLogR"></span> +<DIV class="maxWindowToQuery"><span class="types bigWig"></span> <div class="format"><code>maxWindowToQuery <integer></code></div> <P><I>For bigWigs only</I></P> <P>When signal data is clicked in the Browser image, the details of the signal in the current viewing window are displayed. For bigWigs that reference remote data, the query can be a very expensive operation if the current window is large. To avoid overburdening the Browser, the size of the window to query should be limited. The value of this setting is the maximum window size in bases that should be queried to give the detailed signal numbers.</P> </DIV> <DIV class="negateValues"><span class="types wig bigWig bedGraph"></span> <div class="format"><code>negateValues <on></code></div> <P>Negate the values in the wiggle, meaning that positive values become negative and vice-versa. This is useful for wiggles representing transcription or other activities on the Crick strand. Be aware that wiggles with negative values are drawn in <B>altColor</B> not <B>color</B> as @@ -3364,52 +3415,52 @@ </DIV> <DIV class="autoTranslate"><span class="types genePred"></span> <div class="format"><code>autoTranslate 0</code></div> <P>By default, a predicted protein translation is generated for a gene model when a user views it on the details page. This feature may be blocked by setting <code>autoTranslate</code> to zero.</P> <P><B>Example:</B></P> <pre> autoTranslate 0</pre> <P> The genPred track will NOT show auto-generated protein sequence, perhaps because this track is for RNA genes.</P> </DIV> -<DIV class="intronGap"><span class="types genePred psl"></span> +<DIV class="intronGap"><span class="types genePred bigGenePred psl bigPsl"></span> <div class="format"><code>intronGap <#bases></code></div> <P>In drawing gene models, it can be useful to see "exon arrows" when the transcript extends beyond the current window. This setting, which defaults to zero, ensures that these arrows will not be drawn if the interceding intron gap is less than the stated number of bases.</P> <P><B>Example:</B></P> <pre> intronGap 12</pre> <P>Don't draw exon arrows when the gap between exons is 12 bases or less.</P> </DIV> -<DIV class="defaultLinkedTables"><span class="types genePred"></span> +<DIV class="defaultLinkedTables"><span class="types genePred bigGenePred"></span> <div class="format"><code>defaultLinkedTables <table1>[,table2...]</code></div> <P>In hgTables, when selecting output fields, display these all.joiner-linked tables by default.</P> <P><B>Example:</B></P> <pre> defaultLinkedTables kgXref</pre> </DIV> -<DIV class="idXref"><span class="types genePred"></span> +<DIV class="idXref"><span class="types genePred bigGenePred"></span> <div class="format"><code>idXref <idColumn> <altIdColumn></code></div> <P>By using this setting you can link alternative names to the gene models found in a genePred. This is used by the Table Browser to establish links to other tables.</P> <P><B>Example:</B></P> <pre> track knownGenes idXref kgAlias kgID alias </pre> <P>The ID in the name column of the knownGenes table is related to the alias found in the kgAlias table.</P> </DIV> <DIV class="oldToNew"><span class="types genePred"></span> <div class="format"><code>oldToNew <tableName></code></div> <P>In successive versions of gene models, it can @@ -3748,44 +3799,30 @@ <pre> type psl xeno loxAfr1 otherDb loxAfr1 colorChromDefault off </pre> </DIV> <DIV class="pred"><span class="types psl"></span> <div class="format"><code>pred <assembly.table></code></div> <P>Use the pred setting to name an assembly and table containing protein sequence data for the named alignments.</P> <P><B>Example:</B></P> <pre> pred hg18.blastKGPep04</pre> </DIV> -<DIV class="pslSequence"><span class="types psl"></span> -<div class="format"><code>pslSequence <no/all/different></code></div> - <P>This setting specifies some display configuration options for - psl tracks that also have sequence loaded. - <UL> - <LI><code>all</code>: Display nucleotide labels on all bases.</LI> - <LI><code>different</code>: Label only base differences. </LI> - <LI><code>no</code>: Allow the user to select which of the other two options is preferred.</LI> - </UL> - </P> - <P><B>Example:</B></P> - <pre> pslSequence different</pre> -</DIV> - <DIV class="transMapGene"><span class="types psl"></span> <div class="format"> <code>transMapGene <assembly.table></code><BR> <code>transMapInfo <table></code><BR> <code>transMapSrc <assembly.table></code><BR> <code>transMapTypeDesc <label></code></div> <P>For alignment tracks generated using the TransMap cross-species alignment algorithm, these settings are used to connect the transMap detailed information with the alignments. <UL> <LI><code>transMapInfo</code>: Use to name the table in the current assembly that ties an alignment with the source assembly and feature. </LI> <LI><code>transMapSrc</code>: Use to name the table in the source species assembly that contains the details of the feature's source location. @@ -3922,31 +3959,31 @@ <P><em>Example can be found below.</em></P> </DIV> <DIV class="netAlign"><span class="types netAlign"></span> <div class="format"> <code>type netAlign <otherDb> <otherChainTable></code><BR> <code>otherDb <otherDb></code></div> <P>Tracks of type netAlign show the best chains of sequence alignments from another species to the reference genome. Gaps are filled in levels, where possible. This type requires the assembly database of the other species to be named in both the type setting and in the "<code>otherDb</code>" setting.</P> <P><em>Example can be found below.</em></P> </DIV> -<DIV class="chainColor"><span class="types chain"></span> +<DIV class="chainColor"><span class="types chain bigChain"></span> <div class="format"><code>chainColor <scheme></code></div> <P>By default chains are colored by the alignment chromosome of the query species. This can be overridden with this setting. The three options are:</P> <UL> <LI><code>Chromosome</code> - default</LI> <LI><code>Normalized Score</code> - chains are colored by score</LI> <LI><code>Black</code> - no coloring occurs</LI> </UL> <P>This setting affects <code>chain</code> but not <code>netAlign</code> type tracks.</P> <P><B>Example:</B></P> <pre> chainColor Black</pre> </DIV> @@ -3965,31 +4002,31 @@ <P><B>Example:</B></P> <pre> chainLinearGap medium</pre> </DIV> <DIV class="chainMinScore"><span class="types chain netAlign bed psl"></span> <div class="format"><code>chainMinScore <#></code></div> <P>The chainMinScore setting should reflect the "<code>-minScore</code>" parameter used in axtChain to generate the track. It represents the score threshold for chains to be included in the set. Default is 1000. This setting is for both chain and netAlign type tracks.</P> <P><B>Example:</B></P> <pre> chainMinScore 5000</pre> </DIV> -<DIV class="chainNormScoreAvailable"><span class="types chain netAlign bed"></span> +<DIV class="chainNormScoreAvailable"><span class="types chain bigChain netAlign bed"></span> <div class="format"><code>chainNormScoreAvailable <yes/no></code></div> <P>A given chain or netAlign track may or may not have a populated normScore column. If the column exists, then its value can be displayed in the item details page of the Browser by setting chainNormScoreAvailable to <code>yes</code>. Item coloring based upon score as selected by the <code>chainColor Normalized Score</code> setting also requires this setting to be <code>yes</code>.</P> <P><B>Example:</B></P> <pre> chainNormScoreAvailable yes chainColor Normalized Score </pre> </DIV> <DIV class="matrix"><span class="types chain netAlign bed psl"></span> @@ -4099,160 +4136,163 @@ </DIV> <DIV class="frames"><span class="types wigMaf bigMaf"></span> <div class="format"><code>frames <table/url></code></div> <P>A wigMaf or bigMaf track can display gene codon translation. The reading frame may differ between species. By providing the reading frames information in a separate table, the user can choose which frame to use when viewing the data. For bigMaf the value is expected to be a bigBed, for wigMaf it should be a table. Read about <a href="../bigMaf.html#frames_summary">bigMaf supporting files</a> on the help page.</p> <P><B>Example:</B></P> <pre> frames myCodonFrames</pre> <pre> frames myCodonFrames.bb</pre> </DIV> -<DIV class="irows"><span class="types wigMaf"></span> +<DIV class="irows"><span class="types wigMaf bigMaf"></span> <div class="format"><code>irows off</code></div> <P>By default, gaps in the non-reference species are filled with the placeholder character: <UL> <LI><B>Single Line</B> '<code>-</code>': No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the human genome or a lineage-specific deletion between the aligned blocks in the aligning species.</LI> <LI><B>Double line</B> '<code>=</code>': Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.</LI> <LI><B>Pale yellow coloring</B>: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.</LI> </UL> These display conventions make it easier to visualize the columns in stacked alignments, but they also tend to clutter the display. The user has the option to remove these placeholders by unchecking the "Display chains between alignments" option. To set the default of this option to off, set <code>irows</code> to "<code>off</code>". </P> <P><B>Example:</B></P> <pre> irows off</pre> </DIV> -<DIV class="itemFirstCharCase"><span class="types wigMaf"></span> +<DIV class="itemFirstCharCase"><span class="types wigMaf bigMaf"></span> <div class="format"><code>itemFirstCharCase noChange</code></div> <P>This controls if species names in the multiple alignment should be capitalized in the pairwise display. Set "<code>noChange</code>" to avoid forcing the first letter to lower case. </P> <P><B>Example:</B></P> <pre> itemFirstCharCase noChange</pre> </DIV> -<DIV class="pairwiseHeight"><span class="types wigMaf"></span> +<DIV class="pairwiseHeight"><span class="types wigMaf bigMaf"></span> <div class="format"><code>pairwiseHeight <#></code></div> <P>A wigMaf display in the Browser image is a stacked set of pairwise alignments to the target genome. Using this setting, you can change the height of each pairwise signal in the image.</P> <P><B>Example:</B></P> <pre> pairwiseHeight 10</pre> </DIV> -<DIV class="speciesCodonDefault"><span class="types wigMaf"></span> +<DIV class="speciesCodonDefault"><span class="types wigMaf bigMaf"></span> <div class="format"><code>speciesCodonDefault <species></code></div> <P>This setting, which is used with "frames", declares the default species for the codon reading frame.</P> <P><B>Example:</B></P> <pre> speciesCodonDefault hg19 frames myCodonFrames </pre> </DIV> -<DIV class="speciesDefaultOff"><span class="types wigMaf"></span> +<DIV class="speciesDefaultOff"><span class="types wigMaf bigMaf"></span> <div class="format"><code>speciesDefaultOff <species1> [species2 ...]</code></div> <P>To control which of the stacked pairwise alignments are displayed or hidden by default, use <code>speciesDefaultOff</code> to list the species alignments that will not be displayed. Each species is specified as in the MAF file Organism names except embedded dots and/or spaces are replaced with underscores (e.g. C. elegans -> c_elegans).</P> <P><B>Example:</B></P> <pre> speciesDefaultOff galGal2 fr1 danRer1</pre> </DIV> -<DIV class="speciesOrder"><span class="types wigMaf bed"></span> +<DIV class="speciesOrder"><span class="types wigMaf bigMaf"></span> <div class="format"><I>Related settings:</I><BR> <code>speciesOrder <species1> [species2 …]</code></div> <P>Use <code>speciesOrder</code> to declare the order of the stacked alignments. If there are many species in your track, it may make sense to use the <code>speciesGroups</code> setting instead.</P> </DIV> -<DIV class="speciesLabels"><span class="types wigMaf bed"></span> +<DIV class="speciesLabels"><span class="types wigMaf bigMaf"></span> <div class="format"><code>speciesLabels <species1=newLabel1> [species2=newLabel2 …]</code></div> <P>Use <code>speciesLabels</code> to specify new labels that map to sequence names.</P> <P><B>Example:</B></P> <pre> speciesLabels mm10=mouse_mm10 mm39=mouse_mm39</pre> </DIV> -<DIV class="speciesGroups"><span class="types wigMaf"></span> +<DIV class="speciesGroups"><span class="types wigMaf bigMaf"></span> <div class="format"> <code>speciesGroups <sgroup1> [sgroup2 …]</code><BR> <code>sGroup_<sgroupN> <species1> [species2 …]</code></div> <P>You can include a list of "clades" to group the species into. This option is an alternative to <code>speciesOrder</code>, used when there are many species. Each <code>speciesGroup</code> in the list must have its own setting (sGroup_<group>), followed by a list of species, specified as for speciesOrder.</P> <P><hr class="example" /><B>Examples:</B></P> <pre> speciesOrder panTro1 canFam1 mm5 rn3 \ galGal2 fr1 danRer1 speciesGroups Mammal Vertebrate sGroup_Mammal mm9 rn4 sGroup_Vertebrate galGal2 fr1 danRer1</pre> <P>Choose one of these two alternatives to display species.</P> </DIV> -<DIV class="speciesUseFile"><span class="types wigMaf"></span> -<div class="format"><code>speciesUseFile <fileName></code></div> +<DIV class="speciesUseFile"><span class="types wigMaf bigMaf"></span> +<div class="format"><code>speciesUseFile <cartVariableName></code></div> <P><I>Deprecated</I></P> <P>Much more rarely used, this setting can replace <code>speciesOrder</code> and <code>speciesGroups</code>. - Set the <code>speciesUseFile</code> to a path relative to the apache cgi-bin. - The file should contain a single species name as the first word of each line.</P> + The value is not a file name. It is the name of a cart variable, and the + Browser reads the species list from the file that variable points to. That + file has to be one the Browser itself wrote for this user, so a track cannot + supply it directly; it arrives through the track's own configuration page. + The file holds one species name as the first word of each line.</P> <P><B>Example:</B></P> - <pre> speciesUseFile speciesLists/conserved8Way.txt</pre> + <pre> speciesUseFile myTrack.speciesList</pre> </DIV> <DIV class="summary"><span class="types wigMaf bigMaf"></span> <div class="format"><code>summary <tableName/url></code></div> <P>This setting contains a table name containing a MAF summary table, or a url that points to a bigBed containing that information. The summary view is used when the browser display is zoomed out to contain a million or more basepairs. A summary table is created from a multiple alignment MAF file using the utility <code>hgLoadMafSummary</code> (SQL track) or <code>mafToBigMafSummary</code> (bigMaf). For bigMaf, the value is assumed to be bigBed, Read about <a href="../bigMaf.html#frames_summary">bigMaf supporting files</a> on the help page.</p> <P><B>Example:</B></P> <pre> summary hg17Maf8waySummary</pre> </DIV> -<DIV class="treeImage"><span class="types wigMaf"></span> +<DIV class="treeImage"><span class="types wigMaf bigMaf"></span> <div class="format"><code>treeImage <imageFile></code></div> <P>The phylogenetic tree can used to show the relations of the species in the multiple alignment should be included as an image file. This path is relative to the htdocs images directory (usually /images).</P> <P><B>Example:</B></P> <pre> treeImage phylo/hg17Maf8way.jpg</pre> </DIV> <DIV class="wiggle"><span class="types wigMaf"></span> <div class="format"><code>wiggle <table1> <leftLabel1> <uiLabel1> [table2 leftLabel2 uiLabelN ...]</code></div> <P>Optionally more than one conservation signal can be included with your MAF display by using this setting. When you include conservation wiggles, you @@ -4828,86 +4868,86 @@ for a complete description of how to prepare and display VCF data. </P> </DIV> <DIV class="vcfTabix"><span class="types vcfTabix"></span> <div class="format"><code>type vcfTabix</code></div> <P>If the <code>bigDataUrl</code> setting is included, the data at the location specified by that URL will be displayed. Otherwise, a database table with a single column <code>fileName</code> can specify the location of a local file or a URL. If the database table includes a column <code>seqName</code>, a different VCF file or URL can be specified for each assembly sequence.</P> <P><em>Example can be found below.</em></P> </DIV> -<DIV class="hapClusterEnabled"><span class="types vcf"></span> +<DIV class="hapClusterEnabled"><span class="types vcf vcfTabix"></span> <div class="format"><code>hapClusterEnabled <true|false></code></div> <P>If the VCF file includes genotype columns for at least two individuals, then a haplotype sorting display is enabled by default. This option can be used to disable it if desired, for example if the genotypes have not been phased and a significant portion of the genotypes are heterozygous. More information about the haplotype sorting display can be found on our <A HREF="../hgVcfTrackHelp.html">Configuring VCF tracks</A> page. </P> </DIV> -<div class="hapClusterMethod"><span class="types vcf"></span> +<div class="hapClusterMethod"><span class="types vcf vcfTabix"></span> <div class="format"><code>hapClusterMethod <centerWeighted|fileOrder|treeFile <em>url</em>></code></div> <p>Assuming <code>hapClusterEnabled</code> is <code>true</code>, this specifies how genotypes are ordered for display: <ul> <li><code>centerWeighted</code>: For diploid organisms, this separates the two haplotypes from each sample and dynamically clusters all haplotypes by similarity, weighted by proximity to a central variant. The clustering tree will be drawn in the left label area. This works best for phased genotypes. <li><code>fileOrder</code>: Genotypes are displayed in the order in which they appear in the VCF file. <li><code>treeFile <em>url</em></code>: Genotypes are displayed in the order in which they appear in <code><em>url</em></code>, a <a href="https://en.wikipedia.org/wiki/Newick_format">Newick</a>-formatted tree file whose leaf node IDs are the same as the genotype column IDs in the VCF file. The tree will be drawn in the left label area. </ul> </p> </div> -<DIV class="hapClusterColorBy"><span class="types vcf"></span> +<DIV class="hapClusterColorBy"><span class="types vcf vcfTabix"></span> <div class="format"><code>hapClusterColorBy <altOnly|function|refAlt|base></code></div> <P>Assuming <code>hapClusterEnabled</code> is <code>true</code>, this specifies one of three ways that reference and alternate alleles are colored: <UL> <LI><code>altOnly</code>: reference allele is white (invisible), alternate allele is black. This emphasizes haplotypes with alternate alleles. (default) <LI><code>function</code>: If the <code>geneTrack</code> setting is also provided, then reference allele is white (invisible) and alternate allele is red if the variant changes the protein sequence of a gene, green if the variant falls within a gene but does not change the protein sequence, blue if the variant falls within the UTR of a protein-coding gene or within a non-coding gene, and black if intronic or intergenic. <LI><code>refAlt</code>: reference allele is blue, alternate allele is red. <LI><code>base</code>: A is red, C is blue, G is green and T is magenta. </UL> </P> </DIV> -<div class="geneTrack"><span class="types vcf vcfPhasedTrio"></span> +<div class="geneTrack"><span class="types vcf vcfTabix vcfPhasedTrio"></span> <div class="format"><code>geneTrack <<em>track</em>></code></div> <p>This is for use with <code>hapClusterColorBy function</code>; it specifies the gene track to use when determining the functional effect of each variant.</p> </div> -<DIV class="hapClusterTreeAngle"><span class="types vcf"></span> +<DIV class="hapClusterTreeAngle"><span class="types vcf vcfTabix"></span> <div class="format"><code>hapClusterTreeAngle <triangle|rectangle></code></div> <P>Assuming <code>hapClusterEnabled</code> is <code>true</code>, this controls the shape of leaf clusters on the right of the tree (i.e. the lines drawn to denote groups of identical local haplotypes): <code>triangle</code> for the <B><</B> shape (default), <code>rectangle</code> for the <B>[</B> shape. </P> </DIV> <DIV class="labelFields"><span class="types bigBarChart bigBed bigGenePred bigNarrowPeak bigPsl"></span> <div class="format"><code>labelFields <<EM>fieldName[,fieldName]</EM>></code></div> <P>A list of fields from the bigBed based file that can be used as a label. The special value <B>none</B> can be specified if no labels are desired. </P> </DIV> @@ -4917,53 +4957,53 @@ </P> </DIV> <DIV class="labelSeparator"><span class="types bigBed bigGenePred bigNarrowPeak bigPsl"></span> <div class="format"><code>labelSeparator <<EM>text</EM>></code></div> <P>One or more characters to use as the field separator between multiple labels. A slash (/) by default, this string can have double quotes around it if it should have white spaces in it. </P> </DIV> <DIV class="showSnpWidth"><span class="types halSnake"></span> <div class="format"><code>showSnpWidth <<EM>integer</EM>></code></div> <P>The maximum width (in bases) of a window where the halSnake will show SNPs between the reference and the other species. </P> </DIV> -<DIV class="hapClusterHeight"><span class="types vcf"></span> +<DIV class="hapClusterHeight"><span class="types vcf vcfTabix"></span> <div class="format"><code>hapClusterHeight <<EM>N</EM>></code></div> <P>Assuming <code>hapClusterEnabled</code> is <code>true</code>, this specifies the height in pixels of the haplotype sorting display. </P> </DIV> -<DIV class="applyMinQual"><span class="types vcf"></span> +<DIV class="applyMinQual"><span class="types vcf vcfTabix"></span> <div class="format"><code>applyMinQual <true|false></code></div> <P>If <code>true</code>, then variants whose QUAL column contains a value less than the <code>minQual</code> setting will not be displayed. </P> </DIV> -<DIV class="minQual"><span class="types vcf"></span> +<DIV class="minQual"><span class="types vcf vcfTabix"></span> <div class="format"><code>minQual <<EM>Q</EM>></code></div> <P> <P>Assuming <code>applyMinQual</code> is <code>true</code>, this is the minimum QUAL value required for a variant to be displayed. </P> </DIV> -<DIV class="minFreq"><span class="types vcf"></span> +<DIV class="minFreq"><span class="types vcf vcfTabix"></span> <div class="format"><code>minFreq <<EM>F</EM>></code></div> <P> The minimum minor allele frequency required for a variant to be displayed. By default this is 0.0 (i.e. display all variants). </P> </DIV> <DIV class="vcfDoFilter"><span class="types vcf vcfTabix vcfPhasedTrio"></span> <div class="format"><code>vcfDoFilter <on/off></code></div> <p> Turn on/off the FILTER options available by default for VCF tracks </p> </DIV> <DIV class="vcfDoQual"><span class="types vcf vcfTabix vcfPhasedTrio"></span> @@ -6357,30 +6397,43 @@ <li> <code>tag</code>: Used in the code to select and sort subtracks based upon their membership. Tag names must be alphanumeric, begin with a letter, not contain a period, and be formed such that the desired sort order of the member subtracks will result.</li> <li> <code>title</code>: Label of the subgroup as it appears on the selection matrix that is displayed to the user, e.g.,"Antibody". Spaces within titles must be replaced by '<code>_</code>'. A limited amount of HTML is allowed in titles, such as the insertion of Greek letters using an HTML code. Any use of HTML should be tested to ensure that it displays correctly.</li> </ul> <P>Because subgroup settings are often lengthy, it is recommended that the '<code>\</code>' line continuation character be used to break up the setting over multiple lines for easier reading. </DIV> +<DIV class="noInherit"><span class="types all"></span> +<div class="format"><code>noInherit on</code></div> + <P><I>Deprecated.</I></P> + <P>Placed on a subtrack, this stops the subtrack from taking settings from its composite + parent. Without it a subtrack inherits the parent's <code>type</code> and + <code>group</code>, plus every parent setting the subtrack does not define itself.</P> + <P>The Browser only checks whether the setting is present, so any value turns it on, + including <code>noInherit off</code>. Defining a setting on the subtrack already + overrides the inherited value, so this setting is rarely needed.</P> + <P><B>Example:</B></P> + <pre> noInherit on</pre> +</DIV> + <DIV class="subGroups"><span class="types subGroups"></span> <div class="format"><code>subGroups <gTag1=mTag1?> [gTag2= mTag2?]</code></div> <P>The subtracks themselves declare their membership in a group with the <code>subGroups</code> setting. Each subtrack must declare its membership in all of its composite's subgroups. Notice that membership is declared by pairs of tags: the group tag (e.g. gTag1) is paired with that group's member tag (e.g. mTag1b) as gTag1=mTag1b (cell=K562).</P> </DIV> <DIV class="dimensions"><span class="types subGroups"></span> <div class="format"><code>dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]</code></div> <P>In order to define the type of UI desired for selecting subtracks based upon groups, additional settings are needed at the composite level. For a one- or two-dimensional array of