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/trackDbSettings.yaml src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml index 8e7f1b36c9a..ed148214e8d 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml @@ -25,32 +25,32 @@ - name: type_for_hubs types: - all roles: - super - composite - view - leaf category: Common Settings context: trackDb level: required required: true summary: Declares the format of the data and is used to determine display methods and options. description: 'Declares the format of the data and is used to determine display methods and options. Valid settings for a hub: bam/cram , bigBarChart , bigBed , bigChain , bigGenePred , bigInteract , - bigLolly , bigMaf , bigNarrowPeak , bigPsl , bigWig , halSnake , hic , vcfTabix , vcfPhasedTrio . - Detailed descriptions of each type can be found below. In many cases the type setting includes additional + bigLolly , bigMaf , bigNarrowPeak , bigNet , bigPsl , bigWig , halSnake , hic , vcfTabix , vcfPhasedTrio + . 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.' format: type examples: - type bigBed 6 + - name: shortLabel types: - all roles: - super - composite - view - leaf category: Common Settings context: trackDb @@ -83,56 +83,57 @@ to identify a track. For instance, the long label is displayed above the track's data in the Browser image. This label should be descriptive enough to allow users to uniquely identify the track within the Browser. It is limited to 76 printable characters. Some special characters are allowed in the longLabel. format: longLabel examples: - longLabel Human mRNAs from GenBank - name: bigDataUrl types: - bigBarChart - bigBed - bigChain - bigInteract - bigLolly - bigMaf + - bigNet - bigPsl - bigWig - bam - hic - vcfTabix - vcfPhasedTrio roles: - super - composite - view - leaf category: Common Settings context: trackDb level: required required: true summary: The location of a remote data file containing the bulk of the data for the track. description: 'The location of a remote data file containing the bulk of the data for the track. This setting is required for all data tracks in a track hub. The setting is either the full URL (including http: or another protocol) or it is relative to the directory in which the trackDb file containing this setting is located. The file must be in one of the supported remote data file formats: bam/cram, - bigBarChart, bigBed, bigChain, bigLolly, bigInteract, bigMaf, bigPsl, bigGenePred, bigMethyl, bigNarrowPeak, - bigWig, vcfTabix, or hic. Note that bam/cram and vcfTabix/vcfPhasedTrio types require a separate index - file that must have the same name as the data file plus a standard suffix (".bai" and ".tbi" respectively), - unless bigDataIndex is used. All occurrences of the string $D in the URL will be substituted with - the genome assembly database name. This allows a trackDb entry to be used with for multiple assemblies. - $D substitution is not implemented for track hubs.' + bigBarChart, bigBed, bigChain, bigLolly, bigInteract, bigMaf, bigNet, bigPsl, bigGenePred, bigMethyl, + bigNarrowPeak, bigWig, vcfTabix, or hic. Note that bam/cram and vcfTabix/vcfPhasedTrio types require + a separate index file that must have the same name as the data file plus a standard suffix (".bai" + and ".tbi" respectively), unless bigDataIndex is used. All occurrences of the string $D in the URL + will be substituted with the genome assembly database name. This allows a trackDb entry to be used + with for multiple assemblies. $D substitution is not implemented for track hubs.' format: bigDataUrl <url/relativePath> examples: - bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bb - bigDataUrl biBrainH3K4me1.bb - name: html types: - all roles: - super - composite - view - leaf category: Common Settings context: trackDb level: base @@ -2674,30 +2675,43 @@ - bigChain - bam roles: - leaf category: bigChain - Pairwise Alignments context: trackDb level: full required: false summary: Specifies the default drawing mode. description: Specifies the default drawing mode. The itemBases , itemCodons , diffBases and diffCodons options are applicable only if the track has sequence, as specified by the baseColorUseSequence setting. The genomicCodons , itemCodons and diffCodons are applicable only if the track has CDS info, as specified by the baseColorUseCds setting. format: "baseColorDefault\n <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>" examples: [] +- name: bigNet + types: + - bigNet + roles: + - leaf + category: bigNet - Alignment Nets + context: trackDb + level: new + required: false + summary: '' + description: '' + format: type bigNet targetDb chainTrack + examples: [] - name: bigGenePred types: - bigGenePred roles: - leaf category: bigGenePred - Gene Annotations context: trackDb level: null required: false summary: '' description: '' format: type bigGenePred examples: [] - name: intronGap types: