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/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index 1fc0748b9bd..fc59ea703fb 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -257,31 +257,31 @@ <!-- 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'> + <TR VALIGN=TOP><TD class="type_for_hubs"><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-base">html</code></div> </TD></TR> <TR VALIGN=TOP><TD class="visibility"><A name="visibility"></A><IMG class='toggle detail'> @@ -293,30 +293,39 @@ </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-base">priority <float></code></div> </TD></TR> + <TR VALIGN=TOP><TD class="canPack"><A name="canPack"></A><IMG class='toggle detail'> + <div class="format"><code class="level-deprecated">canPack <off/on></code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="configureByPopup"><A name="configureByPopup"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">configureByPopup <on/off></code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="origAssembly"><A name="origAssembly"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">origAssembly <db></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-full">darkerLabels on</code><BR> </div> </TD></TR> <TR VALIGN=TOP><TD class="dataVersion"><A name="dataVersion"></A><IMG class='toggle detail'> @@ -535,30 +544,35 @@ <div class="format"><code class="level-full"> barChartSizeWindows <largeMax> <smallMin></code> </div> <tr valign=top><td class="barChartStretchToItem"><a name="barChartStretchToItem"></a> <img alt="" class='toggle detail'> <div class="format"><code class="level-new"> barChartStretchToItem on</code> </div> </td></tr> <tr valign=top><td class="barChartFacets"><a name="barChartFacets"></a> <img alt="" class='toggle detail'> <div class="format"><code class="level-new"> barChartFacets on</code> </div> </td></tr> +<tr valign=top><td class="barChartMatrixUrl"><a name="barChartMatrixUrl"></a> + <img alt="" class='toggle detail'> + <div class="format"><code class="level-full">barChartMatrixUrl <url></code> + </div> +</td></tr> <tr valign=top><td class="barChartStatsUrl"><a name="barChartStatsUrl"></a> <img alt="" class='toggle detail'> <div class="format"><code class="level-new"> barChartStatsUrl on</code> </div> </td></tr> <tr valign=top><td class="singleCellColumnNames"><a name="singleCellColumnNames"></a> <img alt="" class='toggle detail'> <div class="format"><code class="level-new"> singleCellColumnNames off</code> </div> </td></tr> <tr valign=top><td class="barChartMerge"><a name="barChartMerge"></a> <img alt="" class='toggle detail'> <div class="format"><code class="level-new"> @@ -739,30 +753,34 @@ <span class="filterLimits"><code class="level-full">filterLimits.<fieldName> <low>[:<high>]</code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="filterText"><A name="filterText"></A> <A name="filterText.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filterText.<fieldName> <default search string></code><BR> <span class="filterType"><code class="level-full">filterType.<fieldName> <wildcard/regexp></code></span></div> </TD></TR> <TR VALIGN=TOP><TD class="filterValues"><A name="filterValues"></A> <A name="filterValues.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filterValues.<fieldName> <value1,value2,value3...></code><BR> <span class="filterValuesDefault"><code class="level-full">filterValuesDefault.<fieldName> <value1,value2,value3...></code></span><BR> <span class="filterType"><code class="level-full">filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd></code></span></div> </TD></TR> + <TR VALIGN=TOP><TD class="filterBy"><A name="filterBy"></A><IMG class='toggle detail'> + <div class="format"> + <code class="level-full">filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]</code></div> + </TD></TR> <TR VALIGN=TOP><TD class="filterLabel"><A name="filterLabel"></A> <A name="filterLabel.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-full">filterLabel.<fieldName> <label></code></div> </TD></TR> <TR VALIGN=TOP><TD class="filterPriority"><A name="filterPriority"></A> <A name="filterPriority.fieldName"></A><IMG class='toggle detail'> <div class="format"> <code class="level-new">filterPriority.<fieldName> <number></code></div> </TD></TR> <TR VALIGN=TOP><TD class="highlight"><A name="highlight"></A> <A name="highlight.fieldName"></A> <A name="highlightLimits.fieldName"></A> <A name="highlightByRange.fieldName"></A><IMG class='toggle detail'> <div class="format"> @@ -847,30 +865,36 @@ bigChain - Genome-wide Pairwise Alignments </TH></TR> <TR VALIGN=TOP><TD class="bigChain"><IMG class='toggle detail'> <div class="format"> <code>type bigChain targetDb</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="linkDataUrl"><A name="linkDataUrl"</A><IMG class='toggle detail'> <div class="format"><code class="level-full">linkDataUrl <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="otherTwoBitUrl"><A name="otherTwoBitUrl"</A><IMG class='toggle detail'> <div class="format"><code class="level-new">otherTwoBitUrl <url/relativePath></code></div> </TD></TR> + <TR VALIGN=TOP><TD class="chainColor"><A name="chainColor"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">chainColor <scheme></code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="chainNormScoreAvailable"><A name="chainNormScoreAvailable"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">chainNormScoreAvailable <yes/no></code></div> + </TD></TR> <TR VALIGN=TOP><TD class="baseColorUseSequence"><A name="baseColorUseSequence"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit ></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorDefault"><A name="baseColorDefault"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></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> @@ -881,30 +905,33 @@ <A name="bigGenePred"></A> <TABLE class="settingsTable" id="bigGenePred_-_Gene_Annotations"> <THEAD><TR><TD><DIV ID="bigGenePred_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigGenePred - Gene Annotations </TH></TR> <TR VALIGN=TOP><TD class="bigGenePred"><IMG class='toggle detail'> <div class="format"> <code>type bigGenePred</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="intronGap"><A name="intronGap"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">intronGap <#bases></code></div> + </TD></TR> <TR VALIGN=TOP><TD class="baseColorDefault"><A name="baseColorDefault"></A><IMG class='toggle detail'> <div class="format"><code class="level-full"> baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLabelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">defaultLabelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelSeparator"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelSeparator <text></code></div> </TD></TR> <tr valign=top><td> <p>Additional settings defined in other sections are also @@ -967,30 +994,48 @@ bigMaf - Multiple alignments </TH></TR> <TR VALIGN=TOP><TD class="bigMaf"><IMG class='toggle detail'> <div class="format"> <code>type bigMaf</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="speciesOrder"><A name="speciesOrder"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">speciesOrder <species1> [species2 …]</code></div> </TD></TR> <TR VALIGN=TOP><TD class="speciesLabels"><A name="speciesLabels"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">speciesLabels <species1=newLabel1> [species2=newLabel2 …]</code></div> </TD></TR> + <TR VALIGN=TOP><TD class="pairwiseHeight"><A name="pairwiseHeight"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">pairwiseHeight <#></code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="speciesGroups"><A name="speciesGroups"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">speciesGroups <sgroup1> [sgroup2 …]</code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="speciesDefaultOff"><A name="speciesDefaultOff"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">speciesDefaultOff <species1> [species2 ...]</code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="speciesCodonDefault"><A name="speciesCodonDefault"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">speciesCodonDefault <species></code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="itemFirstCharCase"><A name="itemFirstCharCase"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">itemFirstCharCase noChange</code></div> + </TD></TR> + <TR VALIGN=TOP><TD class="irows"><A name="irows"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">irows off</code></div> + </TD></TR> <TR VALIGN=TOP><TD class="frames"><A name="frames"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">frames <url/relativePath></code></div> </TD></TR> <TR VALIGN=TOP><TD class="summary"><A name="summary"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">summary <tableName/url></code></div> </TD></TR> </TABLE> <BR><BR> <A name="bigNarrowPeak"></A> <TABLE class="settingsTable" id="bigNarrowPeak_-_Peaks"> <THEAD><TR><TD><DIV ID="bigNarrowPeak_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigNarrowPeak - Peaks </TH></TR> @@ -1026,45 +1071,45 @@ <code>type bigPsl</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="baseColorUseCds"><A name="baseColorUseCds"><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorUseCds <given></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorUseSequence"><A name="baseColorUseSequence"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss ></code></div> </TD></TR> <TR VALIGN=TOP><TD class="baseColorDefault"><A name="baseColorDefault"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons></code></div> </TD></TR> + <TR VALIGN=TOP><TD class="baseColorTickColor"><A name="baseColorTickColor"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">baseColorTickColor <lighterShade/contrastingColor></code></div> + </TD></TR> <TR VALIGN=TOP><TD class="showDiffBasesAllScales"><A name="showDiffBasesAllScales"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">showDiffBasesAllScales on</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="pslSequence"><A name="pslSequence"></A><IMG class='toggle detail'> - <div class="format"><code class="level-new">pslSequence <no/all/different></code></div> - </TD></TR> <TR VALIGN=TOP><TD class="showCdsAllScales"><A name="showCdsAllScales"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showCdsAllScales on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="showCdsMaxZoom"><A name="showCdsMaxZoom"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showCdsMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showDiffBasesMaxZoom"><A name="showDiffBasesMaxZoom"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showDiffBasesMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLabelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">defaultLabelFields <fieldName[,fieldName]></code></div> </TD></TR> @@ -1082,30 +1127,33 @@ <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-base">autoScale <off/on/group></code></div> </TD></TR> + <TR VALIGN=TOP><TD class="mouseOverFunction"><A name="mouseOverFunction"></A><IMG class='toggle detail'> + <div class="format"><code class="level-full">mouseOverFunction <noAverage></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'> @@ -1164,32 +1212,32 @@ <BR><BR> <A name="bigLolly"></A> <TABLE class="settingsTable" id="bigLolly - Lollipop charts"> <THEAD><TR><TD><DIV ID="bigLolly_intro" class="intro"></DIV></TD></TR></THEAD> <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> bigLolly - lollipop graphs </TH></TR> <TR VALIGN=TOP><TD class="bigLolly"><IMG class='toggle detail'> <div class="format"> <code>type bigLolly</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="noStems"><a name="noStems"<a/><img alt="" class='toggle detail'> - <div class="format"><code class="level-full">noStems <on/off></code> + <tr valign=top><td class="lollyNoStems"><a name="lollyNoStems"></a><img alt="" class='toggle detail'> + <div class="format"><code class="level-full">lollyNoStems <on/off></code> </div> </td></tr> <tr valign=top><td class="lollySizeField"><a name="lollySizeField"<a/><img alt="" class='toggle detail'> <div class="format"><code class="level-full">lollySizeField <integer></code> </div> </td></tr> <tr valign=top><td class="lollyMaxSize"><a name="lollyMaxSize"<a/><img alt="" class='toggle detail'> <div class="format"><code class="level-full">lollyMaxSize <integer></code> </div> </td></tr> <tr valign=top><td class="lollyField"><a name="lollyField"<a/><img alt="" class='toggle detail'> <div class="format"><code class="level-full">lollyField <integer></code> </div> </td></tr> <tr valign=top><td class="yAxisLabel"><a name="yAxisLabel"<a/><img alt="" class='toggle detail'> @@ -1780,32 +1828,33 @@ <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> + <TD>bed, bigBed, bigGenePred, psl, bigPsl</TD> + <TD>Replaced with <A onclick="return jumpTo(this);" HREF="#">spectrum</A>, which + sets the same flag and takes the same type list.</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>