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armish code review suggestions
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@piotr-gawron
piotr-gawron committed Jun 15, 2016
1 parent c288d42 commit b7e0d6a
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Showing 3 changed files with 43 additions and 71 deletions.
2 changes: 1 addition & 1 deletion src/main/AbstractFile.js
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Expand Up @@ -2,7 +2,7 @@
* AbstractFile is an abstract representation of a file. There are two implementation:
* 1. RemoteFile - representation of a file on a remote server which can be
* fetched in chunks, e.g. using a Range request.
* 2. LoclaStringFile is a representation of a file that was created from input string.
* 2. LocalStringFile is a representation of a file that was created from input string.
* Used for testing and small input files.
* @flow
*/
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11 changes: 11 additions & 0 deletions src/main/sources/VcfDataSource.js
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Expand Up @@ -104,6 +104,17 @@ function create(data: Object): VcfDataSource {
throw new Error(`Missing URL from track: ${JSON.stringify(data)}`);
}

function create(data: {url?: string, content?: string}): VcfDataSource {
var {url, content} = data;
if (url) {
return createFromVcfFile(new VcfFile(new RemoteFile(url)));
} else if (content) {
return createFromVcfFile(new VcfFile(new LocalStringFile(content)));
}
// If no URL or content is passed, fail
throw new Error(`Missing URL or content from track: ${JSON.stringify(data)}`);
}

module.exports = {
create,
createFromVcfFile
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101 changes: 31 additions & 70 deletions src/test/data/vcf-test.js
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Expand Up @@ -9,24 +9,40 @@ import RemoteFile from '../../main/RemoteFile';
import LocalStringFile from '../../main/LocalStringFile';

describe('VCF', function() {
it('should respond to queries', function() {
var vcf = new VcfFile(new RemoteFile('/test-data/snv.vcf'));
var range = new ContigInterval('20', 63799, 69094);
return vcf.getFeaturesInRange(range).then(features => {
expect(features).to.have.length(6);
describe('should respond to queries', function() {
var testQueries = (vcf) => {
var range = new ContigInterval('20', 63799, 69094);
return vcf.getFeaturesInRange(range).then(features => {
expect(features).to.have.length(6);

var v0 = features[0],
v5 = features[5];

expect(v0.contig).to.equal('20');
expect(v0.position).to.equal(63799);
expect(v0.ref).to.equal('C');
expect(v0.alt).to.equal('T');

var v0 = features[0],
v5 = features[5];
expect(v5.contig).to.equal('20');
expect(v5.position).to.equal(69094);
expect(v5.ref).to.equal('G');
expect(v5.alt).to.equal('A');
});
};

expect(v0.contig).to.equal('20');
expect(v0.position).to.equal(63799);
expect(v0.ref).to.equal('C');
expect(v0.alt).to.equal('T');
var remoteFile = new RemoteFile('/test-data/snv.vcf');

expect(v5.contig).to.equal('20');
expect(v5.position).to.equal(69094);
expect(v5.ref).to.equal('G');
expect(v5.alt).to.equal('A');
it('remote file', function() {
var vcf = new VcfFile(remoteFile);
testQueries(vcf);
});

it('local file from string', function() {
return remoteFile.getAllString().then(content => {
var localFile = new LocalStringFile(content);
var vcf = new VcfFile(localFile);
testQueries(vcf);
});
});
});

Expand All @@ -52,58 +68,3 @@ describe('VCF', function() {
});
});
});
describe('VCF from string content', function() {
var content = '';
before(function() {
content =
"##fileformat=VCFv4.1\n"+
"##source=VarScan2\n"+
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\n"+
"##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\n"+
"##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\n"+
"##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\n"+
"##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\n"+
"##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\n"+
"##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\n"+
"##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\n"+
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"+
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n"+
"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n"+
"##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\n"+
"##FORMAT=<ID=AD,Number=1,Type=Integer,Description=\"Depth of variant-supporting bases (reads2)\">\n"+
"##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\n"+
"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\n"+
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR\n"+
"20 61795 . G T . PASS DP=81;SS=1;SSC=2;GPV=4.6768E-16;SPV=5.4057E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:44:22:22:50%:16,6,9,13 0/1:.:37:18:19:51.35%:10,8,10,9\n"+
"20 62731 . C A . PASS DP=68;SS=1;SSC=1;GPV=1.4855E-11;SPV=7.5053E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:32:17:15:46.88%:9,8,9,6 0/1:.:36:21:15:41.67%:8,13,8,7\n"+
"20 63799 . C T . PASS DP=72;SS=1;SSC=7;GPV=3.6893E-16;SPV=1.8005E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:39:19:19:50%:8,11,11,8 0/1:.:33:12:21:63.64%:5,7,8,13\n"+
"20 65288 . G T . PASS DP=35;SS=1;SSC=0;GPV=7.8434E-5;SPV=8.2705E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:21:13:8:38.1%:4,9,0,8 0/1:.:14:10:4:28.57%:2,8,0,4\n"+
"20 65900 . G A . PASS DP=53;SS=1;SSC=0;GPV=1.5943E-31;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:26:0:26:100%:0,0,12,14 1/1:.:27:0:27:100%:0,0,15,12\n"+
"20 66370 . G A . PASS DP=66;SS=1;SSC=0;GPV=2.6498E-39;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:32:0:32:100%:0,0,11,21 1/1:.:34:0:34:100%:0,0,15,19\n"+
"20 68749 . T C . PASS DP=64;SS=1;SSC=0;GPV=4.1752E-38;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:23:0:23:100%:0,0,7,16 1/1:.:41:0:41:100%:0,0,21,20\n"+
"20 69094 . G A . PASS DP=25;SS=1;SSC=8;GPV=4.2836E-5;SPV=1.5657E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:12:8:4:33.33%:5,3,4,0 0/1:.:13:5:8:61.54%:3,2,6,2\n"+
"20 69408 . C T . PASS DP=53;SS=1;SSC=0;GPV=8.7266E-12;SPV=9.8064E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:27:9:18:66.67%:5,4,9,9 0/1:.:26:15:11:42.31%:6,9,4,7\n"+
"20 75254 . C A . PASS DP=74;SS=1;SSC=9;GPV=7.9203E-12;SPV=1.1567E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:34:22:11:33.33%:13,9,5,6 0/1:.:40:20:20:50%:5,15,14,6\n";
});

it('should respond to queries', function() {
var vcf = new VcfFile(new LocalStringFile(content));
var range = new ContigInterval('20', 63799, 69094);
return vcf.getFeaturesInRange(range).then(features => {
expect(features).to.have.length(6);

var v0 = features[0],
v5 = features[5];

expect(v0.contig).to.equal('20');
expect(v0.position).to.equal(63799);
expect(v0.ref).to.equal('C');
expect(v0.alt).to.equal('T');

expect(v5.contig).to.equal('20');
expect(v5.position).to.equal(69094);
expect(v5.ref).to.equal('G');
expect(v5.alt).to.equal('A');
});
});
});

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