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beautification
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@jrobinso
jrobinso committed Jul 24, 2019
1 parent b2ee09b commit 443d857
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Showing 2 changed files with 75 additions and 100 deletions.
18 changes: 9 additions & 9 deletions js/bam/bamUtils.js
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Original file line number Diff line number Diff line change
Expand Up @@ -34,17 +34,17 @@

var igv = (function (igv) {

var SEQ_DECODER = ['=', 'A', 'C', 'x', 'G', 'x', 'x', 'x', 'T', 'x', 'x', 'x', 'x', 'x', 'x', 'N'];
var CIGAR_DECODER = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', '?', '?', '?', '?', '?', '?', '?'];
var READ_STRAND_FLAG = 0x10;
var MATE_STRAND_FLAG = 0x20;
const SEQ_DECODER = ['=', 'A', 'C', 'x', 'G', 'x', 'x', 'x', 'T', 'x', 'x', 'x', 'x', 'x', 'x', 'N'];
const CIGAR_DECODER = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', '?', '?', '?', '?', '?', '?', '?'];
const READ_STRAND_FLAG = 0x10;
const MATE_STRAND_FLAG = 0x20;

var BAM1_MAGIC_BYTES = new Uint8Array([0x42, 0x41, 0x4d, 0x01]); // BAM\1
var BAM1_MAGIC_NUMBER = readInt(BAM1_MAGIC_BYTES, 0);
const BAM1_MAGIC_BYTES = new Uint8Array([0x42, 0x41, 0x4d, 0x01]); // BAM\1
const BAM1_MAGIC_NUMBER = readInt(BAM1_MAGIC_BYTES, 0);

const DEFAULT_SAMPLING_WINDOW_SIZE = 100;
const DEFAULT_SAMPLING_DEPTH = 1000;
const MAXIMUM_SAMPLING_DEPTH = 2500;
const DEFAULT_SAMPLING_DEPTH = 500;
const MAXIMUM_SAMPLING_DEPTH = 10000;

igv.BamUtils = {

Expand Down Expand Up @@ -408,7 +408,7 @@ var igv = (function (igv) {
reader.samplingDepth = config.samplingDepth === undefined ? DEFAULT_SAMPLING_DEPTH : config.samplingDepth;

if (reader.samplingDepth > MAXIMUM_SAMPLING_DEPTH) {
igv.log("Warning: attempt to set sampling depth > maximum value of 2500");
igv.log("Warning: attempt to set sampling depth > maximum value of " + MAXIMUM_SAMPLING_DEPTH);
reader.samplingDepth = MAXIMUM_SAMPLING_DEPTH;
}

Expand Down
157 changes: 66 additions & 91 deletions js/feature/featureFileReader.js
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,12 @@ var igv = (function (igv) {

let maxSize = "vcf" === self.config.format ? 65000 : 1000
if (index.tabix) {
const bsizeOptions = igv.buildOptions(self.config, {range: {start: index.firstAlignmentBlock, size: 26}});
const bsizeOptions = igv.buildOptions(self.config, {
range: {
start: index.firstAlignmentBlock,
size: 26
}
});
const abuffer = await igv.xhr.loadArrayBuffer(self.config.url, bsizeOptions)
const bsize = igv.bgzBlockSize(abuffer)
maxSize = index.firstAlignmentBlock + bsize;
Expand Down Expand Up @@ -161,15 +166,15 @@ var igv = (function (igv) {
*/
igv.FeatureFileReader.prototype.loadIndex = function () {

var idxFile = this.config.indexURL;
const idxFile = this.config.indexURL;

if (this.filename.endsWith('.gz')) {

if (!idxFile) {
idxFile = this.config.url + '.tbi';
}
return igv.loadBamIndex(idxFile, this.config, true, this.genome);

} else {

if (!idxFile) {
Expand All @@ -179,35 +184,30 @@ var igv = (function (igv) {
}
};

igv.FeatureFileReader.prototype.loadFeaturesNoIndex = function () {
igv.FeatureFileReader.prototype.loadFeaturesNoIndex = async function () {

var self = this;
const options = igv.buildOptions(this.config); // Add oauth token, if any
const data = await igv.xhr.loadString(this.config.url, options)

var options = igv.buildOptions(self.config); // Add oauth token, if any
this.header = this.parser.parseHeader(data);
if (this.header instanceof String && this.header.startsWith("##gff-version 3")) {
this.format = 'gff3';
}
return this.parser.parseFeatures(data); // <= PARSING DONE HERE

return igv.xhr.loadString(self.config.url, options)
.then(function (data) {
self.header = self.parser.parseHeader(data);
if (self.header instanceof String && self.header.startsWith("##gff-version 3")) {
self.format = 'gff3';
}
return self.parser.parseFeatures(data); // <= PARSING DONE HERE
})

};

igv.FeatureFileReader.prototype.loadFeaturesWithIndex = function (chr, start, end) {
igv.FeatureFileReader.prototype.loadFeaturesWithIndex = async function (chr, start, end) {

//console.log("Using index");
var self = this;


var blocks,
tabix = self.index && self.index.tabix,
refId = tabix ? self.index.sequenceIndexMap[chr] : chr,
promises = [];
const config = this.config
const parser = this.parser
const tabix = this.index.tabix
const refId = tabix ? this.index.sequenceIndexMap[chr] : chr
const promises = []

blocks = self.index.blocksForRange(refId, start, end);
const blocks = this.index.blocksForRange(refId, start, end);

if (!blocks || blocks.length === 0) {
return Promise.resolve([]);
Expand All @@ -217,108 +217,83 @@ var igv = (function (igv) {

promises.push(new Promise(async function (fullfill, reject) {

var startPos = block.minv.block,
startOffset = block.minv.offset,
endPos,
options,
success;

if (self.index.tabix) {
const bsizeOptions = igv.buildOptions(self.config, {
range: {
start: block.maxv.block,
size: 26
}
});
const abuffer = await igv.xhr.loadArrayBuffer(self.config.url, bsizeOptions)
const lastBlockSize = igv.bgzBlockSize(abuffer)
const startPos = block.minv.block
const startOffset = block.minv.offset
const endOffset = block.maxv.offset
let endPos

if (tabix) {
let lastBlockSize = 0
if (endOffset > 0) {
const bsizeOptions = igv.buildOptions(config, {
range: {
start: block.maxv.block,
size: 26
}
});
const abuffer = await igv.xhr.loadArrayBuffer(config.url, bsizeOptions)
lastBlockSize = igv.bgzBlockSize(abuffer)
}
endPos = block.maxv.block + lastBlockSize;
} else {
endPos = block.maxv.block;
}

options = igv.buildOptions(self.config, {
options = igv.buildOptions(config, {
range: {
start: startPos,
size: endPos - startPos + 1
}
});

success = function (data) {

var inflated,
slicedData,
slicedFeatures,
filteredFeatures,
f,
i;

if (self.index.tabix) {
inflated = new Uint8Array(igv.unbgzf(data));
} else {
inflated = data;
}

slicedData = startOffset ? inflated.slice(startOffset) : inflated;
slicedFeatures = self.parser.parseFeatures(slicedData);
const success = function (inflated) {
const slicedData = startOffset ? inflated.slice(startOffset) : inflated;
const slicedFeatures = parser.parseFeatures(slicedData);

// Filter features not in requested range.
filteredFeatures = [];
for (i = 0; i < slicedFeatures.length; i++) {
f = slicedFeatures[i];
const filteredFeatures = [];
for (let f of slicedFeatures) {
if (f.start > end) break;
if (f.end >= start && f.start <= end) {
filteredFeatures.push(f);
}
}


fullfill(filteredFeatures);
};


// Async load
if (self.index.tabix) {
if (tabix) {
igv.xhr
.loadArrayBuffer(self.config.url, options)
.then(success)
.loadArrayBuffer(config.url, options)
.then(function (data) {
const inflated = new Uint8Array(igv.unbgzf(data))
success(inflated)
})
.catch(reject);
} else {
igv.xhr
.loadString(self.config.url, options)
.loadString(config.url, options)
.then(success)
.catch(reject);
}

}))
});

return Promise.all(promises)

.then(function (featureArrays) {

var i,
allFeatures;

if (featureArrays.length === 1) {
allFeatures = featureArrays[0];
} else {
allFeatures = featureArrays[0];

for (i = 1; i < featureArrays.length; i++) {
allFeatures = allFeatures.concat(featureArrays[i]);
}
const featureArrays = await Promise.all(promises)

allFeatures.sort(function (a, b) {
return a.start - b.start;
});
}
let allFeatures = featureArrays[0];
if(allFeatures.length > 1) {
allFeatures = featureArrays[0];
for (let i = 1; i < featureArrays.length; i++) {
allFeatures = allFeatures.concat(featureArrays[i]);
}
allFeatures.sort(function (a, b) {
return a.start - b.start;
});
}

return allFeatures;
})
return allFeatures;
}

};
}

igv.FeatureFileReader.prototype.getIndex = function () {

Expand Down

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