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_PairCache.js
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_PairCache.js
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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')
}
}
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',
'JBrowse/Model/SimpleFeature',
],
function(
declare,
Util,
SimpleFeature
) {
return declare(null, {
constructor(args) {
this.featureCache = {}
this.insertUpperPercentile = args.insertUpperPercentile || 0.95
this.insertLowerPercentile = args.insertLowerPercentile || 0.05
this.insertStatsCacheMin = args.insertStatsCacheMin || 400
this.insertMaxSize = args.insertMaxSize || 50000
this.orientationType = args.orientationType || 'fr'
},
// called by getFeatures from the DeferredFeaturesMixin
pairFeatures(query, records, featCallback, endCallback, errorCallback, featTransform) {
const pairCache = {};
for(let i = 0; i < records.length; i++) {
let feat
if (canBePaired(records[i])) {
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]
if(this.insertMaxSize > feat.get('end') - feat.get('start')) {
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(!(records[i]._get('end') < query.start) && !(records[i]._get('start') > query.end)){
let feat = records[i]
featCallback(feat)
}
}
Object.entries(this.featureCache).forEach(([k, v]) => {
if(v._get('end') > query.start && v._get('start') < query.end) {
featCallback(v)
}
})
},
cleanFeatureCache(query) {
Object.entries(this.featureCache).forEach(([k, v]) => {
if((v._get('end') < query.start) || (v._get('start') > query.end)) {
delete this.featureCache[k]
}
})
},
getStatsForPairCache() {
if(Object.keys(this.featureCache).length > this.insertStatsCacheMin) {
var total = Object.keys(this.featureCache).length
var tlens = Object.entries(this.featureCache)
.map(([k, v]) => Math.abs(v.get('template_length')))
.filter(tlen => tlen < this.insertMaxSize)
.sort((a, b) => a - b)
var sum = tlens.reduce((a, b) => a + b, 0)
var sum2 = tlens.map(a => a*a).reduce((a, b) => a + b, 0)
var avg = sum / total;
var sd = Math.sqrt((total * sum2 - sum*sum) / (total * total));
return {
upper: avg + 3*sd,
lower: avg - 3*sd
}
}
return { upper: Infinity, lower: 0 }
}
});
});