6aca098fdf7765a7122271fdcc18d5ddfe468edc max Sun Oct 4 09:59:09 2026 -0700 trackDb docs: maxItems now also sets the VCF record limit of vcfTabix tracks, refs #37306 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index 2bba21bdfcb..640b8e7d94d 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -2345,37 +2345,43 @@ <code>itemRgb off</code>, or by a <code>color</code> setting when neither the track nor its parent says <code>itemRgb on</code>. The currently selected scheme is stored in the cart variable <code><trackName>.colorField</code>. When a non-default scheme is active, the track long label gains a <em>(Coloring by: <label>)</em> suffix. </P> <P><B>Example:</B></P> <pre> colorFields default="Kozak strength" colorByEvidence="Evidence type" colorByHlaClass="HLA class" </pre> <P>This creates a three-option dropdown. <code>colorByEvidence</code> and <code>colorByHlaClass</code> must be extra fields in the bigBed whose values are <code>R,G,B</code> strings.</P> </DIV> -<DIV class="maxItems"><span class="types bed bigBed broadPeak psl"></span> +<DIV class="maxItems"><span class="types bed bigBed broadPeak psl vcfTabix"></span> <div class="format"><code>maxItems <integer></code></div> <P>Maximum number of items to display individually in full or pack or squish mode. When the maximum is 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>For <code>type vcfTabix</code> tracks, <code>maxItems</code> is the maximum number of + VCF records loaded for the current window. If the window holds more, the track asks the + user to zoom in. Without this setting, the limit is the hg.conf setting vcfMaxItems, + 10,000 by default. Raising it lets the haplotype display of a large genotype VCF be + viewed in larger windows, but drawing becomes slow with many samples. + </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 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),