@gmod/jbrowse/src/JBrowse/Store/SeqFeature/_PairCache.js

JBrowse - client-side genome browser

class PairedRead {
    id() {
        return Math.min(this.read1.id(), this.read2.id())
    }
    get(field) {
        return this._get(field.toLowerCase())
    }
    _get(field) {
        if(field === 'start') {
            return Math.min(this.read1._get('start'), this.read2._get('start'))
        } else if(field === 'end') {
            return Math.max(this.read1._get('end'), this.read2._get('end'))
        } else if(field === 'name') {
            return this.read1._get('name')
        } else if(field === 'pair_orientation') {
            return this.read1._get('pair_orientation')
        } else if(field === 'template_length') {
            return this.read1._get('template_length')
        } else if(field === 'is_paired') {
            return true // simply comes from paired end reads
        } else if(field === 'paired_feature') {
            return true // it is a combination of two reads
        }
    }
    pairedFeature() { return true }
    children() {}
}

function canBePaired(alignment) {
    return alignment._get('multi_segment_template') &&
        !alignment._get('multi_segment_next_segment_unmapped') &&
        alignment._get('seq_id') === alignment._get('next_seq_id') &&
        (alignment._get('multi_segment_first') || alignment._get('multi_segment_last')) &&
        !(alignment._get('secondary_alignment') || alignment._get('supplementary_alignment'))
}

define([
    'dojo/_base/declare',
    'JBrowse/Util',
],
function(
    declare,
    Util,
) {

return declare(null, {
    constructor(args) {
        this.featureCache = {}
    },


    pairFeatures(query, records, featCallback, errorCallback) {
        const pairCache = {};
        for(let i = 0; i < records.length; i++) {
            let feat
            if (canBePaired(records[i]) && Math.abs(records[i]._get('template_length')) < query.maxInsertSize) {
                let name = records[i]._get('name')
                feat = pairCache[name]
                if (feat) {
                    if(records[i]._get('multi_segment_first')) {
                        feat.read1 = records[i]
                    } else if(records[i]._get('multi_segment_last')) {
                        feat.read2 = records[i]
                    } else {
                        console.log('unable to pair read',records[i])
                    }
                    if(feat.read1 && feat.read2) {
                        delete pairCache[name]
                        this.featureCache[name] = feat
                    }
                }
                else {
                    feat = new PairedRead()
                    if(records[i]._get('multi_segment_first')) {
                        feat.read1 = records[i]
                    } else if(records[i]._get('multi_segment_last')) {
                        feat.read2 = records[i]
                    } else {
                        console.log('unable to pair read', records[i])
                    }
                    pairCache[name] = feat
                }
            }
            else if(Util.intersect(records[i]._get('start'), records[i]._get('end'), query.start, query.end)) {
                let feat = records[i]
                featCallback(feat)
            }
        }
        // dump paired features
        Object.entries(this.featureCache).forEach(([k, v]) => {
            if(Util.intersect(v._get('start'), v._get('end'), query.start, query.end)) {
                featCallback(v)
            }
        })
        // dump unpaired features from the paircache
        Object.entries(pairCache).forEach(([k, v]) => {
            if(v.read1) {
                if(Util.intersect(v.read1._get('start'), v.read1._get('end'), query.start, query.end)) {
                    featCallback(v.read1)
                }
            }
            else if(v.read2) {
                if(Util.intersect(v.read2._get('start'), v.read2._get('end'), query.start, query.end)) {
                    featCallback(v.read2)
                }
            }
        })
    },


    cleanFeatureCache(query) {
        Object.entries(this.featureCache).forEach(([k, v]) => {
            if(!Util.intersect(v._get('start'), v._get('end'), query.start, query.end)) {
                delete this.featureCache[k]
            }
        })
    }


});
});