353a34ac7e7638457db3f55e57452069113d860b braney Sun Sep 6 13:34:28 2026 -0700 Add a bigNet track type, a net of alignments in a bigBed, refs #20824 Track hubs have had no way to show a real net. The usual stand-in is a net rendered as a maf, which loses the level structure that makes a net useful for establishing orthologous sequence. bigNet holds the netAlign columns in a bigBed, so a hub can carry the net itself. The format is bed6+20: the target in chrom/chromStart/chromEnd, the query sequence in name, the query strand in strand, then level and the rest of the netAlign fields. The trackDb line is type bigNet <targetDb> <chainTrack> mirroring type netAlign. chainTrack is the plain trackDb name of the bigChain track in the same hub; hgc adds the hub prefix itself. chainNetLoadRangeHub() builds a chainNet from a bigBed range query and hands it to the same helpToNet() the SQL path uses, so the nesting is rebuilt the same way. netDraw picks its loader off tg->isBigBed and the drawing code below that is untouched. genericNetClick does the same for the details page and follows the named chain track for the alignment. Also bounds the level walk in helpToNet() by help->maxDepth. It could read one past the end of the levels array. netToBigNet converts a net file to bedToBigBed input. It writes the tab line itself rather than calling bigNetTabOut, because autoSql prints a double with %g and that drops digits off a chain score. diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index b220e727fb4..cd4d9a21d38 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -212,30 +212,31 @@ in the sections below.</I> <OL> <LI><A HREF="#commonSettings">Common trackDb settings</A></LI> <LI><A HREF="#settingsByType">Settings by track type</A> – with examples <UL> <LI><A HREF="#bam">bam/cram</A>: Compressed Sequence Alignment/Map tracks</LI> <LI><A HREF="#bigBed_-_Item_or_Region_Track_Settings">bigBed</A>: Item or region tracks</LI> <LI><A HREF="#bigBarChart">bigBarChart</A>: Bar charts of categorical variables displayed over genomic regions</LI> <LI><A HREF="#bigChain_-_Pairwise_Alignments">bigChain</A>: Genome-wide Pairwise Alignments</LI> <LI><A HREF="#bigGenePred_-_Gene_Annotations">bigGenePred</A>: Gene Annotations</LI> <LI><A HREF="#bigInteract">bigInteract</A>: Pairwise interactions</LI> <LI><A HREF="#bigLolly">bigLolly</A>: Lollipops</LI> <LI><A HREF="#bigNarrowPeak_-_Peaks">bigNarrowPeak</A>: Peaks</LI> <LI><A HREF="#bigMaf_-_Multiple_Alignments">bigMaf</A>: Multiple Alignments</LI> + <LI><A HREF="#bigNet_-_Alignment_Nets">bigNet</A>: Alignment Nets</LI> <LI><A HREF="#bigPsl_-_Pairwise_Alignments">bigPsl</A>: Pairwise Alignments</LI> <LI><A HREF="#bigWig_-_Signal_Graphing_Track_Settings">bigWig</A>: Signal graphing tracks</LI> <LI><A HREF="#hic">hic</A>: Hi-C contact matrices</LI> <LI><A HREF="#halSnake">halSnake</A>: HAL Snake Format</LI> <LI><A HREF="#vcfTabix">vcfTabix</A>: Variant Call Format</LI> <LI><A HREF="#vcfPhasedTrio">vcfPhasedTrio</A>: Variant Call Format Trios</LI> </UL></LI> <LI><A HREF="#groupingTracks">Grouping tracks into sets and hierarchies</A> – with examples <UL> <LI><A HREF="#superTrack">Supertracks (Folders)</A></LI> <LI><A HREF="#compositeTrack">Composite Tracks</A> <UL> <LI><A HREF="#subGroups">Subgroups</A></LI> <LI><A HREF="#view">Views</A></LI> @@ -892,30 +893,49 @@ </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> </TABLE> <BR><BR> +<BR><BR> + +<A name="bigNet"></A> +<TABLE class="settingsTable" id="bigNet_-_Alignment_Nets"> +<THEAD><TR><TD><DIV ID="bigNet_intro" class="intro"></DIV></TD></TR></THEAD> + <TR VALIGN=TOP><TH><IMG class='toggle oneSection'> + bigNet - Alignment Nets + </TH></TR> + <TR VALIGN=TOP><TD class="bigNet"><IMG class='toggle detail'> + <div class="format"> + <code class="level-new">type bigNet targetDb chainTrack</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> +</TABLE> + +<BR><BR> + <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>