var vcfSource = (name, path) => ({
name: name,
viz: pileup.viz.variants(),
data: pileup.formats.vcf({
url: path
})
});
var bamSource = (name, cssClass, path, chunks) => {
var data = pileup.formats.bam({
url: path,
indexUrl: path + '.bai',
indexChunks: chunks
});
return [
{
name, cssClass, data,
viz: pileup.viz.coverage()
},
{
name, cssClass, data,
viz: pileup.viz.pileup()
}
];
};
lazilyCreateDalliance: function() {
if (this.browser) return;
var vcfSource = (name, path) => ({
name: name,
viz: pileup.viz.variants(),
data: pileup.formats.vcf({
url: path
})
});
var bamSource = (name, cssClass, path, chunks) => {
var data = pileup.formats.bam({
url: path,
indexUrl: path + '.bai',
indexChunks: chunks
});
return [
{
name, cssClass, data,
viz: pileup.viz.coverage()
},
{
name, cssClass, data,
viz: pileup.viz.pileup()
}
];
};
var sources = [
{
name: 'Genome',
viz: pileup.viz.genome(),
isReference: true,
data: pileup.formats.twoBit({
url: 'http://www.biodalliance.org/datasets/hg19.2bit'
})
},
{
name: 'Scale',
viz: pileup.viz.scale()
},
{
name: 'Location',
viz: pileup.viz.location()
}
];
// See https://github.com/hammerlab/cycledash/issues/525
if (this.canDisplayPath(this.props.vcfPath)) {
sources.push(vcfSource('Run VCF', this.props.vcfPath));
}
if (this.canDisplayPath(this.props.truthVcfPath)) {
sources.push(vcfSource('Truth VCF', this.props.truthVcfPath));
}
if (this.props.normalBamPath) {
sources = sources.concat(bamSource('Normal', 'normal', this.props.normalBamPath, this.state.normalBaiChunks));
}
if (this.props.tumorBamPath) {
sources = sources.concat(bamSource('Tumor', 'tumor', this.props.tumorBamPath, this.state.tumorBaiChunks));
}
var pileupEl = this.refs.pileupElement;
this.browser = pileup.create(pileupEl, {
range: this.rangeForRecord(this.props.selectedRecord),
tracks: sources
});
},