Configuring a source

General options when configuring a tier

name (required)

The name of the track, as shown in the tier-identification tab.

desc

A longer description of the content, shown when clicking on the tier-identification tab. Currently only plain text supported -- should probably allow a subset of HTML as well (TBD).

disabled

If true, the source is disabled by default (can be manually re-enabled from the track selector).

stylesheet_uri

URI of a DAS Stylesheet to use when displaying this data. For DAS sources, this overrides the source's default stylesheet. For other sources, this allows richer style configuration. More information about Dalliance's implementation of DAS stylesheets can be found here.

style

Array of JSON-encoded style rules.

mapping

Remap the data for this source using a mapping specified in the global chains configuration. See the section on coordinate system mappings for more details.

collapseSuperGroups

Hint to allow more "gene-like" rendering for some data sources. Will probably be deprecated once we find a better way of determining which sources provide gene annotations.

pinned

If true, the tier will be placed in the non-scrolling "pinned" section at the top of the browser.

featureInfoPlugin

Configure a feature-info plugin which just applies to this tier. e.g.:

{name:                'BBD test',
 bwgURI:              'http://www.biodalliance.org/datasets/ensGene.bb',
 collapseSuperGroups: true
 featureInfoPlugin:   function(f, info) {
                          info.add('Testing', 'This is a test');
                      };
}

noSourceFeatureInfo

Disable any feature info plugins that would normally be added by the data source for this tier.

Configuring a DAS source

uri (required)

Base URI for the DAS server. Used to construct URIs for requesting features, sequence, and (if not over-ridden) stylesheets. e.g.

{name:                 'MeDIP raw',
 uri:                  'http://www.derkholm.net:8080/das/medipseq_reads'}

tier_type

Setting this to the string 'sequence' indicates that this should be a DAS sequence tier rather than a DAS features tier.

maxBins

Enables/disables the maxbins DAS extension for server-side downsampling of quantitative data. Default is true.

Configuring a binary sequence source

twoBitURI (required)

URI for the .2bit sequence file. Alternatively, twoBitBlob can be used to configure a local file as the sequence source.

tier_type

Setting this to the string 'sequence' indicates that this is a sequence tier.

Configuring a bigwig or bigbed source

BigWig and BigBed files are configured in the same manner -- Dalliance automatically distinguished between the two when loading. big* sources are recognized by the presence of a bwgURI option in their configuration.

bwgURI (required)

The URI for the big* file. Despite the name, this can be used with both BigWig and BigBed files.

forceReduction

Takes an integer parameter. Forces one of the 'reduced' forms of the data to be used. 0=first reduction, 1=second reduction, etc. Alternatively, a value less than zero can be used to ensure that reduced data is never used.

quantLeapThreshold (currently bigwig only)

Enables leap-by-threshold functionality. Takes a numerical parameter which is the default threshold.

Configuring a BAM source

Dalliance can directly view BAM files so long as they're sorted and indexed. BAM source configurations are recognized by the presence of a bamURI option.

bamURI (required)

URI of a BAM file to access. e.g.

{name: "MyBAMTrack",
 bamURI: "http://server/myfile.sort.bam"}

baiURI

Explicitly specify the URI for the BAM index (.bam.bai) file. If not specified, Dalliance tries appending '.bai' to the value of the bamURI parameter.

Configuring a Tabix source

Dalliance can access Tabix-indexed flatfiles. Currently supported payloads are VCF and BED, but other formats may be added in future.

{name: "Variants",
 uri: "http://server/myfile.vcf.gz",
 tier_type: 'tabix',
 payload: 'vcf'}

Configuring a Memstore source

Dalliance can directly access small textual files (currently supported formats are VCF, BED, and WIG -- more may be added in future). Since these don't support random access, the whole file will be loaded when the track is initialized, hence "memory store" (memstore). Configuration is very similar to tabix

{name: "Variants",
 uri: "http://server/myfile.vcf",
 tier_type: 'memstore',
 payload: 'vcf'}

Configuring a JBrowse-REST source

{name: 'JBTest',
 jbURI: 'http://my.server.com/jbrowse/rest',
 jbQuery: 'type=IntergenicRegion'}

Configuring an Ensembl-REST source

Since Dalliance 0.9, data can be fetched from the Ensembl-REST API.

tier_type: ensembl

Required for Ensembl-REST source configurations

uri

Base URI for the server. Unusually, this is not required for Ensembl-REST sources, and defaults to http://beta.rest.ensembl.org.

species (currently required)

A species name as recognized by the Ensembl-REST API. Future versions may try to work this out automatically from the browser's coordSystem parameter.

type

An array of feature types to fetch.

{name:                 'e! transcripts',
 uri:                  'http://beta.rest.ensembl.org',
 tier_type:            'ensembl',
 species:              'human',
 type:                 ['transcript', 'exon', 'cds']}