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

JBrowse - client-side genome browser

const LRU = cjsRequire('quick-lru')
const { BamFile } = cjsRequire('@gmod/bam')


const bamIndexedFilesCache = new LRU({ maxSize: 5 })

const BlobFilehandleWrapper = cjsRequire('../../Model/BlobFilehandleWrapper')

class BamSlightlyLazyFeature {
    _get_id() { this.record.id() }
    _get_type() { return 'match'}
    _get_score() { return this.record._get('mq')}
    _get_mapping_quality() { return this.record.mappingQuality}
    _get_flags() { return `0x${this.record.flags.toString(16)}`}
    _get_strand() { return this.record.isReverseComplemented() ? -1 : 1 }
    _get_read_group_id() { return this.record.readGroupId }
    _get_seq_id() { return this._store._refIdToName(this.record._refID)}
    _get_qc_failed() { return this.record.isFailedQc()}
    _get_duplicate() { return this.record.isDuplicate()}
    _get_secondary_alignment() { return this.record.isSecondary()}
    _get_supplementary_alignment() { return this.record.isSupplementary()}
    _get_multi_segment_template() { return this.record.isPaired()}
    _get_multi_segment_all_correctly_aligned() { return this.record.isProperlyPaired()}
    _get_multi_segment_all_aligned() { return this.record.isProperlyPaired()}
    _get_multi_segment_next_segment_unmapped() { return this.record.isMateUnmapped()}
    _get_multi_segment_first() { return this.record.isRead1()}
    _get_multi_segment_last() { return this.record.isRead2()}
    _get_multi_segment_next_segment_reversed() { return this.record.isMateReverseComplemented()}
    _get_pair_orientation() { return this.record.getPairOrientation()}
    _get_unmapped() { return this.record.isSegmentUnmapped()}
    _get_next_seq_id() { return this.record.isPaired() ? this._store._refIdToName(this.record._next_refid()) : undefined }
    _get_is_paired() { return this.record.isPaired() }
    _get_next_pos() { return this.record.isPaired() ? this.record._next_pos() : undefined }
    _get_next_segment_position() { return this.record.isPaired()
        ? ( this._store._refIdToName(this.record._next_refid())+':'+(this.record._next_pos()+1)) : undefined}
    _get_tags() { return this.record._tags() }
    _get_seq() { return this.record.getReadBases() }

    constructor(record, store) {
        this.record = record
        this._store = store
    }

    tags() {
        return this._get_tags()
    }

    id() {
        return this.record.id()
    }

    _get(field) {
        const methodName = `_get_${field}`
        if (this[methodName]) return this[methodName]()
        else return this.record._get(field)
    }
    get(field) {
        const methodName = `_get_${field.toLowerCase()}`
        if (this[methodName]) return this[methodName]()
        else return this.record.get(field)
    }

    parent() {}

    children() {}

    pairedFeature() { return false }
}


define( [
            'dojo/_base/declare',
            'JBrowse/Util',
            'JBrowse/Errors',
            'JBrowse/Store/SeqFeature',
            'JBrowse/Store/DeferredStatsMixin',
            'JBrowse/Store/DeferredFeaturesMixin',
            'JBrowse/Store/SeqFeature/IndexedStatsEstimationMixin',
            'JBrowse/Store/SeqFeature/_PairCache',
            'JBrowse/Store/SeqFeature/_SpanCache',
            'JBrowse/Store/SeqFeature/_InsertSizeCache',
            'JBrowse/Model/XHRBlob',
            'JBrowse/Model/SimpleFeature',
        ],
        function(
            declare,
            Util,
            Errors,
            SeqFeatureStore,
            DeferredStatsMixin,
            DeferredFeaturesMixin,
            IndexedStatsEstimationMixin,
            PairCache,
            SpanCache,
            InsertSizeCache,
            XHRBlob,
            SimpleFeature
        ) {

return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, IndexedStatsEstimationMixin ], {
    constructor( args ) {

        let dataBlob
        if (args.bam)
            dataBlob = new BlobFilehandleWrapper(args.bam)
        else if (args.urlTemplate)
            dataBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.urlTemplate || 'data.bam'), { expectRanges: true }))
        else throw new Error('must provide either `bam` or `urlTemplate`')

        let baiBlob, csiBlob
        if (args.bai)
            baiBlob = new BlobFilehandleWrapper(args.bai)
        else if (args.csi)
            csiBlob = new BlobFilehandleWrapper(args.csi)
        else if (args.baiUrlTemplate)
            baiBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.baiUrlTemplate)))
        else if (args.csiUrlTemplate)
            csiBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.csiUrlTemplate)))
        else if (args.urlTemplate)
            baiBlob = new BlobFilehandleWrapper(new XHRBlob(this.resolveUrl(args.urlTemplate+'.bai')))
        else throw new Error('no index provided, must provide a BAI or CSI index')

        this.source = dataBlob.toString()

        // LRU-cache the BAM object so we don't have to re-download the
        // index when we switch chromosomes
        const cacheKey = `data: ${dataBlob}, index: ${csiBlob||baiBlob}`
        this.bam = bamIndexedFilesCache.get(cacheKey)
        if (!this.bam) {
            this.bam = new BamFile({
                bamFilehandle: dataBlob,
                baiFilehandle: baiBlob,
                csiFilehandle: csiBlob,
                renameRefSeqs: n => this.browser.regularizeReferenceName(n),
                fetchSizeLimit: args.fetchSizeLimit || 100000000,
                chunkSizeLimit: args.chunkSizeLimit || 20000000
            })

            bamIndexedFilesCache.set(cacheKey, this.bam)
        }

        // pre-download the index before running the statistics estimation so that the stats
        // estimation doesn't time out
        this.bam.hasRefSeq(0)
            .then(() => this.bam.getHeader())
            .then((header) => this._setSamHeader(header))
            .then((res) => {
                this._deferred.features.resolve({success:true});
            })
            .then(() => this._estimateGlobalStats())
            .then(stats => {
                this.globalStats = stats;
                this._deferred.stats.resolve({success:true});
            })
            .catch(err => {
                this._deferred.features.reject(err)
                this._deferred.stats.reject(err)
            })

        this.insertSizeCache = new InsertSizeCache(args);
        this.pairCache = new PairCache(args);
        this.spanCache = new SpanCache(args);
    },

    // process the parsed SAM header from the bam file
    _setSamHeader(samHeader) {
        this._samHeader = {}

        // use the @SQ lines in the header to figure out the
        // mapping between ref seq ID numbers and names
        const refSeqIdToName = []
        const refSeqNameToId = {}
        const sqLines = samHeader.filter(l => l.tag === 'SQ')
        sqLines.forEach((sqLine, seqId) => {
            sqLine.data.forEach(item => {
                if (item.tag === 'SN') {
                    // this is the seq name
                    const seqName = item.value
                    refSeqNameToId[seqName] = seqId
                    refSeqIdToName[seqId] = seqName
                }
            })
        })
        if (refSeqIdToName.length) {
            this._samHeader.refSeqIdToName = refSeqIdToName
            this._samHeader.refSeqNameToId = refSeqNameToId
        }
    },

    _refNameToId(refName) {
        // use info from the SAM header if possible, but fall back to using
        // the ref seq order from when the browser's refseqs were loaded
        if (this._samHeader.refSeqNameToId)
            return this._samHeader.refSeqNameToId[refName]
        else
            return this.browser.getRefSeqNumber(refName)
    },

    _refIdToName(refId) {
        // use info from the SAM header if possible, but fall back to using
        // the ref seq order from when the browser's refseqs were loaded
        if (this._samHeader.refSeqIdToName) {
            return this._samHeader.refSeqIdToName[refId]
        } else {
            let ref = this.browser.getRefSeqById(refId)
            return ref ? ref.name : undefined
        }
    },

    /**
     * Interrogate whether a store has data for a given reference
     * sequence.  Calls the given callback with either true or false.
     */
    hasRefSeq( seqName, callback, errorCallback ) {
        seqName = this.browser.regularizeReferenceName( seqName );

        this._deferred.stats
        .then(() => this.bam.hasRefSeq(this._refNameToId(seqName)))
        .then(callback, errorCallback)
    },

    // called by getFeatures from the DeferredFeaturesMixin
    _getFeatures( query, featCallback, endCallback, errorCallback ) {
        let seqName = query.ref || this.refSeq.name
        seqName = this.browser.regularizeReferenceName( seqName );
        const pairCache = {};
        query.maxInsertSize = query.maxInsertSize||50000

        this.bam.getRecordsForRange(seqName, query.start, query.end, { viewAsPairs: query.viewAsPairs, viewAsSpans: query.viewAsSpans, maxInsertSize: query.maxInsertSize })
            .then(records => {
                if(query.viewAsPairs) {
                    const recs = records.map(f => this._bamRecordToFeature(f))
                    recs.forEach(r => this.insertSizeCache.insertFeat(r))
                    this.pairCache.pairFeatures(query, recs, featCallback, endCallback, errorCallback)
                } else if(query.viewAsSpans) {
                    const recs = records.map(f => this._bamRecordToFeature(f))
                    recs.forEach(r => this.insertSizeCache.insertFeat(r))
                    this.spanCache.pairFeatures(query, recs, featCallback, endCallback, errorCallback)
                } else {
                    for(let i = 0; i < records.length; i++) {
                        this.insertSizeCache.insertFeat(records[i]);
                        featCallback(this._bamRecordToFeature(records[i]))
                    }
                }
                endCallback()
            }).catch(errorCallback)
    },


    getInsertSizeStats() {
        return this.insertSizeCache.getInsertSizeStats()
    },

    cleanFeatureCache(query) {
        this.pairCache.cleanFeatureCache(query)
        this.spanCache.cleanFeatureCache(query)
    },

    cleanStatsCache() {
        this.insertSizeCache.cleanStatsCache()
    },


    _bamRecordToFeature(record) {
        return new BamSlightlyLazyFeature(record, this)
    },

    saveStore() {
        return {
            urlTemplate: this.config.bam.url,
            baiUrlTemplate: (this.config.bai||{}).url,
            csiUrlTemplate: (this.config.csi||{}).url
        };
    }

});
});