@gmod/jbrowse
Version:
JBrowse - client-side genome browser
379 lines (343 loc) • 45.3 kB
JavaScript
require([
'dojo/aspect',
'dojo/_base/declare',
'dojo/_base/array',
'JBrowse/Browser',
'JBrowse/FeatureFiltererMixin',
'JBrowse/Store/SeqFeature/BAM',
'JBrowse/Model/XHRBlob',
'JBrowse/Store/SeqFeature/_MismatchesMixin',
'JBrowse/View/Track/_AlignmentsMixin',
'JBrowse/Model/SimpleFeature'
], function( aspect, declare, array, Browser, FeatureFiltererMixin, BAMStore, XHRBlob, MismatchesMixin, AlignmentsMixin, SimpleFeature ) {
// function distinctBins( features ) {
// var bins = {};
// features.forEach( function(f) {
// bins[ f.data._bin ] = ( bins[ f.data._bin ] || 0 ) + 1;
// });
// return bins;
// }
describe( 'BAM mismatches test', function() {
var feature=new SimpleFeature({data: {
start: 7903922,
length: 90,
cigar: "89M2741N1M",
md: "89A0",
seq: "TACTTGATAAATCAGCTCACTCTCTGGTGCTTTTTAGAGAAGTCCCTGATTCCTTCTTAAACTTGGAATGATAGATGAAATTCACACCCG"
}});
//Config workaround since we aren't directly instantiating anything with Browser/config
var Config=declare(null, {
constructor: function() {
this.config={};
}
});
//Use Config workaround
var MismatchParser = declare([Config, MismatchesMixin, FeatureFiltererMixin]);
it('getMismatches test', function() {
var parser = new MismatchParser();
var obj = parser._getMismatches(feature);
expect(obj[1].base).toEqual("G");
expect(obj[1].length).toEqual(1);
expect(obj[1].start).toEqual(2830)
expect(obj[1].type).toEqual("mismatch");
});
});
describe( 'BAM with volvox-sorted.bam', function() {
var b;
beforeEach( function() {
b = new BAMStore({
browser: new Browser({ unitTestMode: true }),
bam: new XHRBlob('../../sample_data/raw/volvox/volvox-sorted.bam'),
bai: new XHRBlob('../../sample_data/raw/volvox/volvox-sorted.bam.bai'),
refSeq: { name: 'ctgA', start: 1, end: 500001 }
});
});
it( 'constructs', function() {
expect(b).toBeTruthy();
});
it( 'loads some data', function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
b.getFeatures({ start: 0, end: 50000 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
expect(features.length).toBeGreaterThan(1000);
});
});
});
describe( 'BAM with test_deletion_2_0.snps.bwa_align.sorted.grouped.bam', function() {
var b;
beforeEach( function() {
b = new BAMStore({
browser: new Browser({ unitTestMode: true }),
bam: new XHRBlob('../data/test_deletion_2_0.snps.bwa_align.sorted.grouped.bam'),
bai: new XHRBlob('../data/test_deletion_2_0.snps.bwa_align.sorted.grouped.bam.bai'),
refSeq: { name: 'Chromosome', start: 1, end: 20000 }
});
});
it( 'constructs', function() {
expect(b).toBeTruthy();
});
it( 'loads some data', function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
b.getFeatures({ start: 17000, end: 18000 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
expect(features.length).toEqual(124);
//console.log( distinctBins(features) );
});
});
it( 'check that seqlength == seq.length', function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
b.getFeatures({ start: 17000, end: 18000 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
expect(array.every(features,function(feature) { return feature.get('seq_length')== feature.get('seq').length; })).toBeTruthy();
});
});
});
describe( 'empty BAM', function() {
var b;
beforeEach( function() {
b = new BAMStore({
browser: new Browser({ unitTestMode: true }),
bam: new XHRBlob('../data/empty.bam'),
bai: new XHRBlob('../data/empty.bam.bai'),
refSeq: { name: 'Chromosome', start: 1, end: 20000 }
});
});
it( 'constructs', function() {
expect(b).toBeTruthy();
});
it( "returns no data, but doesn't crash", function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
b.getFeatures( { start: 0, end: 50000 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
expect(features.length).toEqual( 0 );
});
});
});
describe( 'BAM with B tags', function() {
var b;
beforeEach( function() {
b = new BAMStore({
browser: new Browser({ unitTestMode: true }),
bam: new XHRBlob('../data/Btag.bam'),
bai: new XHRBlob('../data/Btag.bam.bai'),
refSeq: { end: 1000000,
length: 1000000,
name: "chr1",
seqChunkSize: 80000,
start: 0
}
});
});
it( 'constructs', function() {
expect(b).toBeTruthy();
});
it( 'loads some data', function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
b.getFeatures({ start: 980654, end: 981663 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
//ZC:B:i,364,359,1,0 ZD:B:f,0.01,0.02,0.03 ZE:B:c,0,1,2,3 ZK:B:s,45,46,47
var ret = features[1].get('ZD').split(",");
expect(features[1].get('ZC')).toEqual("364,359,1,0");
expect(features[1].get('ZE')).toEqual("0,1,2,3");
expect(features[1].get('ZK')).toEqual("45,46,47");
expect(Math.abs(+ret[0]-0.01)<Number.EPSILON);
expect(Math.abs(+ret[1]-0.02)<Number.EPSILON);
expect(Math.abs(+ret[2]-0.03)<Number.EPSILON);
expect(features.length).toEqual(2);
//console.log( distinctBins(features) );
});
});
});
describe( 'BAM with tests/data/final.merged.sorted.rgid.mkdup.realign.recal.bam', function() {
var b;
beforeEach( function() {
b = new BAMStore({
browser: new Browser({ unitTestMode: true }),
bam: new XHRBlob('../data/final.merged.sorted.rgid.mkdup.realign.recal.bam'),
bai: new XHRBlob('../data/final.merged.sorted.rgid.mkdup.realign.recal.bam.bai'),
refSeq: { end: 27682,
length: 27682,
name: "chr21_gl000210_random",
seqChunkSize: 80000,
start: 0
}
});
});
it( 'constructs', function() {
expect(b).toBeTruthy();
});
it( 'loads some data', function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
b.getFeatures({ start: 16589, end: 18964 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
expect(features.length).toEqual(281);
//console.log( distinctBins(features) );
});
});
});
describe( 'BAM mismatch test', function() {
var b;
//Config workaround since we aren't directly instantiating anything with Browser/config
var Config=declare(null, {
constructor: function() {
this.config={renderAlignment: {singleline: true}};
}
});
//Use Config workaround
var MismatchParser = declare([Config, MismatchesMixin, FeatureFiltererMixin]);
//Use Config workaround
var AlignmentParser = declare([Config, AlignmentsMixin, FeatureFiltererMixin]);
it('resultTable test', function() {
var parser = new AlignmentParser();
var elt = dojo.create('div');
var res = parser._renderTable(elt, new MismatchParser(), new SimpleFeature({data: {id: "read162/ctgA:g2.t1", seq: "TACACAAGCACCGGGCGCGCGAGACACGATTGAATCCTTCAAACAGGGTTACTCGTTCGTGACAACCGATTACAGCATTCTTAACGTGGTACGTGCACAT", md: "77G18", cigar: "4S22M50N74M"}}));
expect(res.val1).toEqual("TACACAAGCACCGGGCGCGCGAGACA..................................................CGATTGAATCCTTCAAACAGGGTTACTCGTTCGTGACAACCGATTACAGCATTCTTAACGTGGTACGTGCACAT");
expect(res.val2).toEqual(" |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||");
expect(res.val3).toEqual("....CAAGCACCGGGCGCGCGAGACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGATTGAATCCTTCAAACAGGGTTACTCGTTCGTGACAACCGATTACAGCATTCTGAACGTGGTACGTGCACAT");
});
it('resultTable test insertion', function() {
var parser = new AlignmentParser();
var elt = dojo.create('div');
var res = parser._renderTable(elt, new MismatchParser(), new SimpleFeature({data: {id: "ctgA_15155_15557_3:0:1_0:0:0_1dde", seq: "TTTAGTGGGACCCAATCGCAACCCTGCTCCCCTCCCTTACGCCTTATACACTTCAGTGTAAATTCATGCGTTCAGCGAACAACTGGACTTCTGTTGTACG", md: "11A45C41", cigar: "9M1I90M"}}));
expect(res.val1).toEqual("TTTAGTGGGACCCAATCGCAACCCTGCTCCCCTCCCTTACGCCTTATACACTTCAGTGTAAATTCATGCGTTCAGCGAACAACTGGACTTCTGTTGTACG");
expect(res.val2).toEqual("||||||||| || ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||");
expect(res.val3).toEqual("TTTAGTGGG-CCAAATCGCAACCCTGCTCCCCTCCCTTACGCCTTATACACTTCAGTGCAAATTCATGCGTTCAGCGAACAACTGGACTTCTGTTGTACG");
});
it('resultTable test large deletion', function() {
var parser = new AlignmentParser();
var elt = dojo.create('div');
var res = parser._renderTable(elt, new MismatchParser(), new SimpleFeature({data: {seq: "TGATGAGGTCCCTACAAAATCCTATGCTCCCTGCGAATTACAACTCACAGTAAGAAGGGTCACTCTACCAGCGGGGTTAAATATACCGGCCGACTGTCTC", md: "50^agaacagcctaggctttcttagttattgatgcacattctactgacgaacgcagcattcgaactaaaccattggtaatgtaattgtgacacgtgggaatctatttaaagctgcaagaactccaccacgtgttcatccacatcggtctctgtggaatggtccaggaccgtcccaatagggggaattgcgagacccaactaatcgagtgattgaacatgggagcaattcccgaatagaaacttgcaacgcgcagtactacgacgatggtagcaataacgacgcgctacttcagctcatgggtctaaattagggcgaacgattgcacctaatctgctggcttctctagattgtagatccacagggccaattaacagtgcaaagaatagcgtcatatgattagtttgaaaataatatacatgaaaatcgagcacccgcatcaataagctacgagagtctttggagagtgccaatacacctagcacatgctgtgcttatgttatgaaaattcatacttgactaacgttagccaccagccgatggcgctgtcacaacgaccctgggttaccgtttagttctc50", cigar: "50M575D50M"}}));
expect(res.val1).toEqual("TGATGAGGTCCCTACAAAATCCTATGCTCCCTGCGAATTACAACTCACAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAGAAGGGTCACTCTACCAGCGGGGTTAAATATACCGGCCGACTGTCTC");
expect(res.val2).toEqual("|||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||");
expect(res.val3).toEqual("TGATGAGGTCCCTACAAAATCCTATGCTCCCTGCGAATTACAACTCACAGagaacagcctaggctttcttagttattgatgcacattctactgacgaacgcagcattcgaactaaaccattggtaatgtaattgtgacacgtgggaatctatttaaagctgcaagaactccaccacgtgttcatccacatcggtctctgtggaatggtccaggaccgtcccaatagggggaattgcgagacccaactaatcgagtgattgaacatgggagcaattcccgaatagaaacttgcaacgcgcagtactacgacgatggtagcaataacgacgcgctacttcagctcatgggtctaaattagggcgaacgattgcacctaatctgctggcttctctagattgtagatccacagggccaattaacagtgcaaagaatagcgtcatatgattagtttgaaaataatatacatgaaaatcgagcacccgcatcaataagctacgagagtctttggagagtgccaatacacctagcacatgctgtgcttatgttatgaaaattcatacttgactaacgttagccaccagccgatggcgctgtcacaacgaccctgggttaccgtttagttctcTAAGAAGGGTCACTCTACCAGCGGGGTTAAATATACCGGCCGACTGTCTC");
});
it('resultTable long read', function() {
var parser = new AlignmentParser();
var elt = dojo.create('div');
var res = parser._renderTable(elt, new MismatchParser(), new SimpleFeature({
data: {
seq: "TAAGGGCAAGTGGCCGCAACAACTGCGATTACTGACCAACTTGAGTGAGAACTAAGCCTTGAAGCATAGTAGTTGCAATGTTGTAGAAAAGTATACATGTGACAAAAGACAGGGCCTGGTGTCAAGTGTCCTCAGTGATCTGGATAATCATCACGCCTTGTTAGCAGGATTTACCCGCATAGTAATGGCCGGACTTTATATTGCCCTGCTGCGCTAGCTAGTACTGCGGAGGCTCTCTCCCCCTAATTGATATCCGGGCAAGAATGCGCGGGTAGTCAGCATTCATGTCAGTGCTTCTATCAACGTCCTCATTCACCTTGGAAGTGTTGACCTACAGTGTTAAGAGGCAATGTAGCCCGAGACGCCCGTTCAAAGACAAAGCTCCCTGTAATTAAACAGACACCGGTTATGGAGAGTGTGAGTAAGTGACTTCCGACCAGTGTTTGGTATTACAGCCTGGTCCGGTTAACCTCGCAGGGCTAGGAGAATGAGCGCTAGATAGGTGATTACCGAAGTCTCCCCAAAAGGGAACAGTCTTATTAGAGTAGAGAATGTCAAATAGCGTTTATTGAGTTCTGTCTACTGCCCTACCAAGAGCATGCACCAGAGATGCGTCGCAGTCGTAGCGGTAGACGTCGTAATGACCCAGGTGGCGTTCGCGACCTATTCGCGTCGGACGCGCGCGCTACTACAACGAAGGGGTCTGAAAGTGCATGTTCACACTGAAATTCTAGTGTTAGTAAACAAACGCGTGTATTCCAGGGTCGTGTGTGACATTATATGGCTGTCTGCGCCCCTCAATGATCATCCAAGACGTTCAATTGTATCGTTAACGTAGATATCAGGTTTACGTTATCCGTATACTTATTTACGCCGCGCGCTTGAACAGATTCTCCTAACAGCCCTCGCGGTTTCAAAAAGAATCCAAAGTCTACGTACCATCCTTGTTCCAATTCTGCCTGGTTGCGGAGAAAAGATCCGCCTCCGATTACGTACCCGACTCGGTATTGGTAAGTGGGGAAGCAGTCGAACGCATATTTCTTGTTGGTTATATCACAGGCCACGTTTATATCCGGAAGTGGCCGGGATTACGATTTGACGTTCTATCCCCGAGAGCGCATTCTTGTTTGTTACGTACTACCACGCGGGCGCTTCTTATTCCCAGACCAGAGGGAATGTGCGGAAGCTTCTTTCCACAGATTGGCGGAACTTCCGCGTGCTTAGTGCAGGCGGAGAACGTCCGTTCAGTGGTGCGGCTTTATTTTCAATCTGACCCGACCTGCGCTCAAGAGTTGACTAAGTTGTTGTGCGCCCCGAGTAATAGGCGACTCGTCGCAATGGGTCTGGTACATTTAGCATTTTCATCGGTACTGGCGCTTCATAAAGTGCGGCAAATTTCTCACCCCAGTACTCATGTTTATTAGGGTATCAGGACCCGAAGCTTCTCTGTTCCAAAGAAATGTACTGTTTGCTCCCCTGTCCATCATTTGGAGGAGATCACTTGTGGATTCATGCAATGATGAATGATAAGTTTGGTGCTCCCCACCCGGGGCGCTCTCCAAAAGAGTGAGCAATTTGAACATTTAAATTGCTATTCCAACCCGGAGTCCTGACCGGAACAGTAATGAAACTTCAACCATGCCGTGACAGACTAGAAGAAGGGAAAGTGCTTGTATATGGGAGTAAAATGATGTTGGTGCCGTAATGGTGCCGGGAAGTACTATAGACGCATGTCGTGACGCACCGAGGTAGGCAGTGCTATAATCGTACTGATCCTTCAGGCGCCGCCGGACCTACGAAGCTGAGATTAGACACCGGCACACTAGCCCCGTCAGCGACGGCTGCGCGGCCGTAGCCCTGCAGCGGAATGGGGCTAACACGCATAAACGCCCGCATAACCACTCGAGTCTACGGGAGATTCACTCAGGCTGTTTGCTTCGAACGTGTAGTCTCATTACATAATTCATAATACCTCCAAGACCAACGGCTGCTCATGACTCTCTTACCTTGTTAGAGGACATTTCGGCACTAGGGAAGAGTACTGAGGACTTTGAAAACGTCGATAAAACCATCGCGGGAACTAGACTAGCGTTAGACACTCCATATTTTACGGGTCGCAAGCTTGAGGTCACTGTCCCGGCCAGCTGCAAGTGCTACGGCAGGAGGGGATCTACCTAACGTGCAGTAAACGAGCCCTTGCCCAGTAATGAGGCGTACTCCGTCTCTAATCGTCAGTAAGTTACATGTCCGAGGACGCCCTCTACGAGTTGAACTCTGGCTACGGCACCACCTGTCGCGCGCCCTGCTCGGGTCCCCATCTTGCTTATCCAAACTCACCTCGCCTTACGGAATCTCTGGTTGCCAGTCATCCGATGGTCATTGAAGCAGCCGTGGTACATCGTAGCCAGATACTTCCAGGGCGGCCAGCCATATTCCTACAGCCAAGTCGGCTGCATAATTACAGCGCCTGGCACGGACTAATACGATCCCACAAGCCTGGTAGATGACCCTTAGACACCTAAAGCGCCCTCTGACCTATCTGCACGTGATACTTGATTTTTTGTCAATGAGCGGACAGGTAGATGACTAATATCACAGGTGTCGTCTAGGTTTGCACAATGTCAGCACGACTCATCCCGCAAGGCCCGGACGGCTGACTCACATCAGCTAGCTCCATCTCCCTCAGCAGCACTAAGATTCCCACGTGACCAGGGCGACGGGCCTCAGCCAAACGTATCCTTGATATCTACTTAAGTCAAGGTTGACTCCGAACCCTATGGGTCGGTAGCCGTTAACAGGGAGTCTATATCTCGGCGTTCCATTGCTTGTTTCAAACTACTGCTATAAGGTGAAAGCGCTGGAGGGCATAGTATTATGCCCAAAGTTGCGCGTAGATCCGTCGGGATATGTTGCTATAATAAGGACTGCTTCGAGAGTAGGCGGTAACGGCCTCCCGCCTTCAGTGGCGCGGAACATCGAATCGGAGTTACAAGCGACTTGACCGATGTCATGATCCAAGTTTATGTTACCCGATCGGATCCGGATGCTCGATCGTGCGACGAGGTCGGAAAGACGGACGAAATACGATTCAACCGCGCGCAACTCATTAGCATCTAACCTTTAGCCTCACATGGGTGTTAACGTGGTGGGCTCACTCGGCGTACTCTTTGTGCACTATTCGCGTATAGAACAACAGCTCAAGTTGCGACATGATGCTCTTACGTGATTCCCACAGTTTCCCACCTCAGGATGCTTTCTTTAGCTAAAAGCCCAATAGTTATGGGCGGCACCTTCCAGACTCCCACGAGGACGGCTATGACGTTGCTAAACCATCGCCGCCAAAGGCTAGCGCTAACGAGTTCTGTGAGTTTGTTCCGGGCCAGATCTCCAGAGATGGTCGCAACAACGCAGTACCGGTCTTTATACTGGTGACCCTCTACCTGTATTAAGTTAAGCGTTGTCCTACGTACATGGTCGTGAGTACCTCGCGTAGCTCAAACGCCAACGGCACTAGCAGCGAGAATTATTGTCGCGATACTTACTACAATACTTTACCCGATATTGACGTGCAGGGTTGAAAGACGATGGGACAGTTGAATATCCTATTTTGACGGAATCCTCAAAACTCCCTCCACCTCAGGTACGGCCCTGTCCGGGACCGCATTCTTGCATATATTGGGTCCCAGAGCGTATCTAAGTTAGTTCTCTTGACCGTTCACCGACTCATAGGGCGACTCGTTATCGCCCTCCGAAACCGATAGCTTCGTTACCTCAGAATGATGACAGAGCCTGTAACGTAGAGTGATCCCAATCTCACTCGTGCCTTGTCCACCGTTCCGTGAAGACGAAGCAATACGCGGAATACGTGGCTTCGTAATATTTTGACGATATGGGGGCTGGGACGCGTCAAGACTTCCATGACAAACAAAGTGAAGAGCAACTGCATACCCTCATCATGAGTCACTATTACCAGAGGTAGCGATGGAAACGCTAATTTGGGTCAGGGCAGCTATCGCAGTCCCGCAGGTGTAGGCGCGAAGACTTTTTCTTTTGTTGCGGAGTTGATCAAGGTAATCTCACGGTATAAGCACGGTTATTTACGCCAAGCGACGTCCCTGGGAGATCCGCCCACGTAGGGACCCCATAATCCATAAATGACCTGCGTCGAAACCTTCATATCGTGACAGAACCGCTTTCCTAGGGATGACGGTCCCCGCATTCAGAGTTCTGACTTTGGCCAGCGTGTAGACTTAACAACTCCACTTACGCGGTACATTGAAGTCCCGTTCAGTCCAGTGTGACCTGTGTACTCGAATAACGTGTAGACCAGCGCGTCTACGACTTAGCGCGGCTCCACTCCAAGAGCACCTTTTGGAACTTTCGCAACGAGCGCTGTTGGCCGTTAAGCGGTATTTCACAAATAGATCACCCTAGTGTCGGTAAACCGACTACCCTATTGGGATCATCGTGAGCTCGAAACACTAGAGGCGGACCAACGGATATGACATTGATTCGGCTCTACAGAGCTTTCGCCCAGAGGAAAAACTGTGGCAATCTACGCTCGCGGGGGAATTGACTTTAGCGGCCCCTTAGACAGGTGTGGGACACTAGTCTAGATTCACGTCCTACACGACATAACAGCACTTCCTGGCCAGCCCAGAAATAGTACCTGGACGACATCCAGCCTTCCGACGCCATAATGTGGAGCCGTAGCGCCCACGACGATCAACGAGGAGAAATTTACAAAAGGCTGTGTGAATGCTACGTCGTCTACCATTGCCTCATCGAAACGAACGCAACGCACAGCATACAACGTTTTACCATGCCGGAGCGGGATTCCTCAAGTACAGAAGAACAGAGGTCTAAACATGATCCTGAACAAATCGGTGGTTTACACAGCTACCTCAGTCGCATTGGCGTACTGCATCGATCGTGCTTAATCTACGGTCATGCCGGCCCGCGATGCACGTACGAATGGAATACCCTGTCTGCCCCCGCGCGAGTTACGCTGTCTCGCACATACCGAGCACTTGTCGTTCGAAGCTAAACTATGAGCCCACCGAGCTCCTTATGGCCGCAACCGCGGTGCGGCCAGCTGATAAATTTCCACAGAACACGATCCTCGTGTAAGATCTCGCGGCATAGTAAGTCATTTTCACATGGTTAGGAGAGATAGAATACATGGTTCTGGTAGCTCAACCAGGCATTTGTGGAACCACTTGGCCCTTGGTGAGTGCTAACAATAAAATTCTCCGTATGGGACCAACCAAAGGGTGCTGGATGTGACTTCCCGGCCCAGGTTAGATGTCCATATCATTCATATCATTGCCCGACCGACCCAATGCCTACAATCGATGATGGCGCCTTAGCTAGTTCTTGAGTGTGCCACGTGCCGGCCACGCAGACACGACCCTGCGGCGAGTGATCACCATTACCGGGATTGGCATCGAAGTCTTTTTCTGGGAAGTTAGCCAGTTGAGTGTGCGGTGGCTTAGAATCTCTATTCCCACGTCAAACGCCCCTGGGACGATATTGCTTAACCCTAGTTGGCCACCACCGGAACCATCTTACGGGAGAGCTAGAGCACAGATCCGAGGTTAGATATGTTAGCGTCTCTCGTGAGTCTGAAATGTATCACTTCACCGCGAGAATAGCGCGAATGTCTGTTTGCCCTGGACCATGACGGATTGGCTTAAAAGCACGCTAGTAGCATTTTGGTACGGTTTCCGATCCCGCGATCGTAATTACCTATCTAGGTTATCGCTAG",
md: "24^a196^g7^t15^t60^c163^t24^c4^g61a14^c1^c97^t29^a145^g64^c111^c142^a41^t10^t26^g171^g22^t25^a40^g9^ta95^t16^a34^g81a45^c31^a297^c44^t65^a19^t98^c114^a18^g53^g19^t179c121^a81^t118^a152^t110^t9^c180^a38^t79^t212^t35^c92^a38^g191^a12g127^t21^g111^c237^a165^g24^t27^t255^t95^t70g120^a15^a23t36",
cigar: "7=1I9=1I8=1D10=2I32=1I4=1I20=1I10=1I37=1I83=1I1D7=1D8=1I7=1D7=1I30=1I14=1I9=1D6=1I3=1I8=1I6=1I19=1I17=1I5=1I1=1I23=1I10=1I24=1I2=1I6=1I2=1I31=1D5=1I19=1D3=1I1=1D17=1I25=1I19=1X14=1D1=1D26=1I30=1I1=1I36=1I4=1D29=1D45=2I30=1I17=1I22=1I15=1I16=1D40=1I10=2I14=1D27=1I8=1I1=1I53=3I22=1D6=1I12=1I47=1I54=1I20=1I3=1D41=1D10=1D25=1I1=1D3=1I1=1I14=1I40=2I16=1I26=1X21=1I49=1D14=1I1=1I7=1D16=1I9=1D7=1I18=1I12=1I3=1D9=2D72=1I23=1D16=1D30=1I4=1D8=1I18=1I1=1I20=1I2=1I32=1X35=1I10=1D1=1I10=1I20=1D22=1I8=1I15=1I8=1I20=1I51=1I24=2I43=1I2=1I8=1I33=1I10=1I44=1I9=1D1I5=1I15=1I24=1D15=1I22=1I3=1I9=1I16=1D7=1I11=1I1=1D48=1I7=1I17=1I1=1X4=1I7=1I13=1D1I1=2I6=1I28=1I6=1I31=1I1=1I41=1D2=1I3=1I13=1D15=1I5=1I21=1I3=1I2=1I1=1I6=1D19=1D7=1I122=1I50=1X33=1I37=1I18=1I5=1I14=1I14=1D10=1I15=1I2=1I11=1I5=1I38=1D3=1I14=1I30=1I3=1I25=1I43=1D7=1I5=1I9=1I67=1I3=1I14=1I9=1I38=1D59=1I26=1I25=1D9=1D31=1I8=1I10=2I2=1I41=1I31=1I5=1I13=1I39=1D36=1I2=1D21=1I22=1I28=1I4=1I4=1D10=1I1=1I9=1I1=1I10=1I95=1I9=1I40=1I12=1I15=1I10=1D12=1I18=1I5=1I1D11=1I1=1I19=1I7=1I2=1I33=1I19=1D15=1I18=1I2=1I3=1D34=1I8=1I22=1I15=1I36=1I1=1I25=1I50=1I1D1I12=1X6=1I8=1I51=1I56=2I6=1D21=1D4=1I5=1I29=1I20=1I53=1D59=1I42=1I33=1I36=1I19=1I14=1I22=1I12=1D18=1I3=1I28=2I34=1I55=1I27=1D22=1I2=1D21=1I6=1D1=1I23=1I14=1I51=1I12=1I21=1I23=1I58=1I25=1I4=1I1=1I2=1I20=1D12=1I22=1I21=1I40=1D1=1I10=1I10=1I8=1I20=1I5=1I11=1I5=1I1X13=1I8=1I4=1I2=1I1=1I6=1I19=1I30=1I6=1I24=2I7=1D13=1I2=1D4=1I16=1I3=1X4=1I5=1I27="
}
}));
expect(res.val1).toEqual("TAAGGGCAAGTGGCCGCAACAACTGC-GATTACTGACCAACTTGAGTGAGAACTAAGCCTTGAAGCATAGTAGTTGCAATGTTGTAGAAAAGTATACATGTGACAAAAGACAGGGCCTGGTGTCAAGTGTCCTCAGTGATCTGGATAATCATCACGCCTTGTTAGCAGGATTTACCCGCATAGTAATGGCCGGACTTTATATTGCCCTGCTGCGCTAGCTAGTACTGCGGA-GGCTCTC-TCCCCCTAATTGATAT-CCGGGCAAGAATGCGCGGGTAGTCAGCATTCATGTCAGTGCTTCTATCAACGTCCTCATTCAC-CTTGGAAGTGTTGACCTACAGTGTTAAGAGGCAATGTAGCCCGAGACGCCCGTTCAAAGACAAAGCTCCCTGTAATTAAACAGACACCGGTTATGGAGAGTGTGAGTAAGTGACTTCCGACCAGTGTTTGGTATTACAGCCTGGTCCGGTTAACCTCGCAGGGCTAGGAGAATGAGC-GCTAGATAGGTGATTACCGAAGTCT-CCCCA-AAAGGGAACAGTCTTATTAGAGTAGAGAATGTCAAATAGCGTTTATTGAGTTCTGTCTACTGCCCTACCAAGAGCATG-C-ACCAGAGATGCGTCGCAGTCGTAGCGGTAGACGTCGTAATGACCCAGGTGGCGTTCGCGACCTATTCGCGTCGGACGCGCGCGCTACTACAACGAAGGGGT-CTGAAAGTGCATGTTCACACTGAAATTCT-AGTGTTAGTAAACAAACGCGTGTATTCCAGGGTCGTGTGTGACATTATATGGCTGTCTGCGCCCCTCAATGATCATCCAAGACGTTCAATTGTATCGTTAACGTAGATATCAGGTTTACGTTATCCGTATACTTATTTACGCCGCGCGCTT-GAACAGATTCTCCTAACAGCCCTCGCGGTTTCAAAAAGAATCCAAAGTCTACGTACCATCCTTGTTC-CAATTCTGCCTGGTTGCGGAGAAAAGATCCGCCTCCGATTACGTACCCGACTCGGTATTGGTAAGTGGGGAAGCAGTCGAACGCATATTTCTTGTTGGTTATATCACAGGCCACGTT-TATATCCGGAAGTGGCCGGGATTACGATTTGACGTTCTATCCCCGAGAGCGCATTCTTGTTTGTTACGTACTACCACGCGGGCGCTTCTTATTCCCAGACCAGAGGGAATGTGCGGAAGCTTCTTTCCACAGATTGGCGGAACTTCC-GCGTGCTTAGTGCAGGCGGAGAACGTCCGTTCAGTGGTGCG-GCTTTATTTT-CAATCTGACCCGACCTGCGCTCAAGAG-TTGACTAAGTTGTTGTGCGCCCCGAGTAATAGGCGACTCGTCGCAATGGGTCTGGTACATTTAGCATTTTCATCGGTACTGGCGCTTCATAAAGTGCGGCAAATTTCTCACCCCAGTACTCATGTTTATTAGGGTATCAGGACCCGAAGCTTCTCTGTTCCAAAGAAATGTACTGTTT-GCTCCCCTGTCCATCATTTGGAGG-AGATCACTTGTGGATTCATGCAATGA-TGAATGATAAGTTTGGTGCTCCCCACCCGGGGCGCTCTCCAAA-AGAGTGAGC--AATTTGAACATTTAAATTGCTATTCCAACCCGGAGTCCTGACCGGAACAGTAATGAAACTTCAACCATGCCGTGACAGACTAGAAGAAGGGAAAGT-GCTTGTATATGGGAGT-AAAATGATGTTGGTGCCGTAATGGTGCCGGGAAGT-ACTATAGACGCATGTCGTGACGCACCGAGGTAGGCAGTGCTATAATCGTACTGATCCTTCAGGCGCCGCCGGACCTACGAAGCTGAGATTAGACACCGGCACACTAGCCCCGTCAGCGACGGCTGCGCGGCCG-TAGCCCTGCAGCGGAATGGGGCTAACACGCATA-AACGCCCGCATAACCACTCGAGTCTACGGGAGATTCACTCAGGCTGTTTGCTTCGAACGTGTAGTCTCATTACATAATTCATAATACCTCCAAGACCAACGGCTGCTCATGACTCTCTTACCTTGTTAGAGGACATTTCGGCACTAGGGAAGAGTACTGAGGACTTTGAAAACGTCGATAAAACCATCGCGGGAACTAGACTAGCGTTAGACACTCCATATTTTACGGGTCGCAAGCTTGAGGTCACTGTCCCGGCCAGCTGCAAGTGCTACGGCAGGAGGGGATCTACCTAACGTGCAGTAAACGAGCCC-TTGCCCAGTAATGAGGCGTACTCCGTCTCTAATCGTCAGTAAGTTAC-ATGTCCGAGGACGCCCTCTACGAGTTGAACTCTGGCTACGGCACCACCTGTCGCGCGCCCTGCTCGGGT-CCCCATCTTGCTTATCCAAAC-TCACCTCGCCTTACGGAATCTCTGGTTGCCAGTCATCCGATGGTCATTGAAGCAGCCGTGGTACATCGTAGCCAGATACTTCCAGGGCGGCCAGCCATATTCC-TACAGCCAAGTCGGCTGCATAATTACAGCGCCTGGCACGGACTAATACGATCCCACAAGCCTGGTAGATGACCCTTAGACACCTAAAGCGCCCTCTGACCTATCTGCACGTGATACTTGATT-TTTTGTCAATGAGCGGACAG-GTAGATGACTAATATCACAGGTGTCGTCTAGGTTTGCACAATGTCAGCACGACTCATCC-CGCAAGGCCCGGACGGCTG-ACTCACATCAGCTAGCTCCATCTCCCTCAGCAGCACTAAGATTCCCACGTGACCAGGGCGACGGGCCTCAGCCAAACGTATCCTTGATATCTACTTAAGTCAAGGTTGACTCCGAACCCTATGGGTCGGTAGCCGTTAACAGGGAGTCTATATCTCGGCGTTCCATTGCTTGTTTCAAACTACTGCTATAAGGTGAAAGCGCTGGAGGGCATAGTATTATGCCCAAAGTTGCGCGTAGATCCGTCGGGATATGTTGCTATAATAAGGACTGCTTCGAGAGTAGGCGGTAACGGCCTCCCGCCTTCAGT-GGCGCGGAACATCGAATCGGAGTTACAAGCGACTTGACCGATGTCATGATCCAAGTTTATGTTACCCGATCGGATCCGGATGCTCG-ATCGTGCGACGAGGTCGGAAAGACGGACGAAATACGATTCAACCGCGCGCAACTCATTAGCATCTAACCTTTAGCCTCACATGGGTGTTAACGTGGTGGGCTCACTCGGCGTACTCTTTGTGC-ACTATTCGCGTATAGAACAACAGCTCAAGTTGCGACATGATGCTCTTACGTGATTCCCACAGTTTCCCACCTCAGGATGCTTTCTTTAGCTAAAAGCCCAATAGTTATGGGCGGCACCTTCCAGACTCCCACGAGGACGGCTATGACGTTGCTAAACCA-TCGCCGCCAAAGGCTAGCGCTAACGAGTTCTGTGAGTTTGTTCCGGGCCAGATCTCCAGAGATGGTCGCAACAACGCAGTACCGGTCTTTATACTGGTGACCCTCTACCTGT-ATTAAGTTA-AGCGTTGTCCTACGTACATGGTCGTGAGTACCTCGCGTAGCTCAAACGCCAACGGCACTAGCAGCGAGAATTATTGTCGCGATACTTACTACAATACTTTACCCGATATTGACGTGCAGGGTTGAAAGACGATGGGACAGTTGAATATCCTATTTTGACGGAATCCTCAAAACTCCCTCCACCTCAGGT-ACGGCCCTGTCCGGGACCGCATTCTTGCATATATTGGGT-CCCAGAGCGTATCTAAGTTAGTTCTCTTGACCGTTCACCGACTCATAGGGCGACTCGTTATCGCCCTCCGAAACCGATAGCTT-CGTTACCTCAGAATGATGACAGAGCCTGTAACGTAGAGTGATCCCAATCTCACTCGTGCCTTGTCCACCGTTCCGTGAAGACGAAGCAATACGCGGAATACGTGGCTTCGTAATATTTTGACGATATGGGGGCTGGGACGCGTCAAGACTTCCATGACAAACAAAGTGAAGAGCAACTGCATACCCTCATCATGAGTCACTATTACCAGAGGTAGCGATGGA-AACGCTAATTTGGGTCAGGGCAGCTATCGCAGTCCCGC-AGGTGTAGGCGCGAAGACTTTTTCTTTTGTTGCGGAGTTGATCAAGGTAATCTCACGGTATAAGCACGGTTATTTACGCCAAGCGACGTCCCTGGGAG-ATCCGCCCACGTAGGGACCCCATAATCCATAAATGACCTGC-GTCGAAACCTTCATATCGTGACAGAACCGCTTTCCTAGGGATGACGGTCCCCGCATTCAGAGTTCTGACTTTGGCCAGCGTGTAGACTTAACAACTCCACTTACGCGGTACATTGAAGTCCCGTTCAGTCCAGTGTGACCTGTGTACTCGAATAACGTGTAGACCAGCGCGTCTACGACTTAGCGCGGCTCCACTCCAA-GAGCACCTTTTGGAACTTTCGCAACGAGCGCTGTTGGCCGTTAAGCGGTATTTCACAAATAGATCACCCTAGTGTCGGTAAACCGACTACCCTATTGGGATCATCGTGAGCTCGAAACACTAGAGGCGGACCAACGGATATGACAT-TGATTCGGCTCTACAGAGCTT-TCGCCCAGAGGAAAAACTGTGGCAATCTACGCTCGCGGGGGAATTGACTTTAGCGGCCCCTTAGACAGGTGTGGGACACTAGTCTAGATTCACGTCCTACACGACATAACAGCAC-TTCCTGGCCAGCCCAGAAATAGTACCTGGACGACATCCAGCCTTCCGACGCCATAATGTGGAGCCGTAGCGCCCACGACGATCAACGAGGAGAAATTTACAAAAGGCTGTGTGAATGCTACGTCGTCTACCATTGCCTCATCGAAACGAACGCAACGCACAGCATACAACGTTTTACCATGCCGGAGCGGGATTCCTCAAGTACAGAAGAACAGAGGTCTAAACATGATCCTGAACAAATCGGT-GGTTTACACAGCTACCTCAGTCGCATTGGCGTACTGCATCGATCGTGCTTAATCTACGGTCATGCCGGCCCGCGATGCACGTACGAATGGAATACCCTGTCTGCCCCCGCGCGAGTTACGCTGTCTCGCACATACCGAGCACTTGTCGTTCGAAGCTAAACTATGAGCCCA-CCGAGCTCCTTATGGCCGCAACCGC-GGTGCGGCCAGCTGATAAATTTCCACAG-AACACGATCCTCGTGTAAGATCTCGCGGCATAGTAAGTCATTTTCACATGGTTAGGAGAGATAGAATACATGGTTCTGGTAGCTCAACCAGGCATTTGTGGAACCACTTGGCCCTTGGTGAGTGCTAACAATAAAATTCTCCGTATGGGACCAACCAAAGGGTGCTGGATGTGACTTCCCGGCCCAGGTTAGATGTCCATATCATTCATATCATTGCCCGACCGACCCAATGCCTACAATCGATGATGGCGCCTTAGCTAGTTCTTG-AGTGTGCCACGTGCCGGCCACGCAGACACGACCCTGCGGCGAGTGATCACCATTACCGGGATTGGCATCGAAGTCTTTTTCTGGGAAGTTAGCCAGTT-GAGTGTGCGGTGGCTTAGAATCTCTATTCCCACGTCAAACGCCCCTGGGACGATATTGCTTAACCCTAGTTGGCCACCACCGGAACCATCTTACGGGAGAGCTAGAGCACAGATCCGAGGTTAGATATGTTAGCGTCTCTCGTGAGTCTGAAATGTATCACTTCACCGCGAGAATAGCGCGAATGTCTGTTTGCCCTGGACCATGACGGA-TTGGCTTAAAAGCACG-CTAGTAGCATTTTGGTACGGTTTCCGATCCCGCGATCGTAATTACCTATCTAGGTTATCGCTAG");
expect(res.val2).toEqual("||||||| ||||||||| |||||||| |||||||||| |||||||||||||||||||||||||||||||| |||| |||||||||||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||| ||||||| ||||||| |||||||||||||||||||||||||||||| |||||||||||||| ||||||||| |||||| ||| |||||||| |||||| ||||||||||||||||||| ||||||||||||||||| ||||| | ||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||| || |||||| || ||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||| ||| | ||||||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||||| |||||||||||||| | |||||||||||||||||||||||||| |||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||| ||||||||||||||| |||||||||||||||| |||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||||||||| ||||||||||||||||||||||||||| |||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| ||| ||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||||||| | ||| | |||||||||||||| |||||||||||||||||||||||||||||||||||||||| |||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| | ||||||| |||||||||||||||| ||||||||| ||||||| |||||||||||||||||| |||||||||||| ||| ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||| |||||||||||||||||||||||||||||| |||| |||||||| |||||||||||||||||| | |||||||||||||||||||| || |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||| | |||||||||| |||||||||||||||||||| |||||||||||||||||||||| |||||||| ||||||||||||||| 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||||| |||||||||||||| |||||||||||||| |||||||||| ||||||||||||||| || ||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||| |||||||||||||| |||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||| ||||| ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||||||| ||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||| ||||||||| ||||||||||||||||||||||||||||||| |||||||| |||||||||| || ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| ||||| ||||||||||||| ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||| |||| |||| |||||||||| | ||||||||| | |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| 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expect(res.val3).toEqual("TAAGGGC-AGTGGCCGC-ACAACTGCaGATTACTGAC--ACTTGAGTGAGAACTAAGCCTTGAAGCATAGT-GTTG-AATGTTGTAGAAAAGTATAC-TGTGACAAAA-ACAGGGCCTGGTGTCAAGTGTCCTCAGTGATCTGGAT-ATCATCACGCCTTGTTAGCAGGATTTACCCGCATAGTAATGGCCGGACTTTATATTGCCCTGCTGCGCTAGCTAGTACTGCGG-gGGCTCTCtTCCCCCTA-TTGATATtCCGGGCA-GAATGCGCGGGTAGTCAGCATTCATGTCAG-GCTTCTATCAACGT-CTCATTCACcCTTGGA-GTG-TGACCTAC-GTGTTA-GAGGCAATGTAGCCCGAGA-GCCCGTTCAAAGACAAA-CTCCC-G-AATTAAACAGACACCGGTTATGG-GAGTGTGAGT-AGTGACTTCCGACCAGTGTTTGGT-TT-CAGCCT-GT-CGGTTAACCTCGCAGGGCTAGGAGAATGAGCtGCTAG-TAGGTGATTACCGAAGTCTcCCC-AgAAAGGGAACAGTCTTAT-AGAGTAGAGAATGTCAAATAGCGTT-ATTGAGTTCTGTCTACTGCaCTACCAAGAGCATGcCcACCAGAGATGCGTCGCAGTCGTAGCG-TAGACGTCGTAATGACCCAGGTGGCGTTCG-G-CCTATTCGCGTCGGACGCGCGCGCTACTACAACGAA-GGGTtCTGAAAGTGCATGTTCACACTGAAATTCTaAGTGTTAGTAAACAAACGCGTGTATTCCAGGGTCGTGTGTGACAT--TATGGCTGTCTGCGCCCCTCAATGATCATC-AAGACGTTCAATTGTAT-GTTAACGTAGATATCAGGTTTA-GTTATCCGTATACTT-TTTACGCCGCGCGCTTgGAACAGATTCTCCTAACAGCCCTCGCGGTTTCAAAAAGAA-CCAAAGTCTA--TACCATCCTTGTTCcCAATTCTGCCTGGTTGCGGAGAAAAGA-CCGCCTCC-A-TACGTACCCGACTCGGTATTGGTAAGTGGGGAAGCAGTCGAACGCATATTTCT---TGGTTATATCACAGGCCACGTTcTATATC-GGAAGTGGCCGG-ATTACGATTTGACGTTCTATCCCCGAGAGCGCATTCTTGTTTGTTAC-TACTACCACGCGGGCGCTTCTTATTCCCAGACCAGAGGGAATGTGCGGAAGCTT-TTTCCACAGATTGGCGGAAC-TCCaGCGTGCTTAGTGCAGGCGGAGAACGTCCGTTCAGTGGTGCGtGCTTTATTTTtCAATCTGACCCGACCTGCGCTCAAG-GgTTG-C-AAGTTGTTGTGCGC-CCGAGTAATAGGCGACTCGTCGCAATGGGTCTGGTACATT--GCATTTTCATCGGTAC-GGCGCTTCATAAAGTGCGGCAAATTTCTCACCCCAGTACTCATGTTTA-TAGGGTATCAGGACCCGAAGCTTCTCTGTTCCAAAGAAATGTACTGTTTgGCTCCCCTGTCCAT-A-TTGGAGGtAGATCACTTGTGGATT-ATGCAATGAaTGAATGA-AAGTTTGGTGCTCCCCAC-CGGGGCGCTCTC-AAAgAGAGTGAGCtaAATTTGAACATTTAAATTGCTATTCCAACCCGGAGTCCTGACCGGAACAGTAATGAAACTTCAACCATGCCG-GACAGACTAGAAGAAGGGAAAGTtGCTTGTATATGGGAGTaAAAATGATGTTGGTGCCGTAATGGTGCCGG-AAGTgACTATAGA-GCATGTCGTGACGCACCG-G-TAGGCAGTGCTATAATCGTA-TG-TCCTTCAGGCGCCGCCGGACCTACGAAGCTGAaATTAGACACCGGCACACTAGCCCCGTCAGCGACGG-TGCGCGGCCGcT-GCCCTGCAGC-GAATGGGGCTAACACGCATAaAACGCCCGCATAACCACTCGAG-CTACGGGA-ATTCACTCAGGCTGT-TGCTTCGA-CGTGTAGTCTCATTACATAA-TCATAATACCTCCAAGACCAACGGCTGCTCATGACTCTCTTACCTTGTTAG-GGACATTTCGGCACTAGGGAAGAG--CTGAGGACTTTGAAAACGTCGATAAAACCATCGCGGGAACTAG-CT-GCGTTAGA-ACTCCATATTTTACGGGTCGCAAGCTTGAGGTC-CTGTCCCGGC-AGCTGCAAGTGCTACGGCAGGAGGGGATCTACCTAACGTGCAGT-AACGAGCCCc-TGCCC-GTAATGAGGCGTACT-CGTCTCTAATCGTCAGTAAGTTACtATGTCCGAGGACGCC-TCTACGAGTTGAACTCTGGCTA-GGC-CCACCTGTC-CGCGCCCTGCTCGGGTaCCCCATC-TGCTTATCCAA-CtTCACCTCGCCTTACGGAATCTCTGGTTGCCAGTCATCCGATGGTCATT-AAGCAGC-GTGGTACATCGTAGCCA-ATACTT-CAGGGCG-CCAGCCATATTCCc-A--GCCAAG-CGGCTGCATAATTACAGCGCCTGGCACG-ACTAAT-CGATCCCACAAGCCTGGTAGATGACCCTTAG-C-CCTAAAGCGCCCTCTGACCTATCTGCACGTGATACTTGATTaTT-TGT-AATGAGCGGACAGgGTAGATGACTAATAT-ACAGG-GTCGTCTAGGTTTGCACAATG-CAG-AC-A-TCATCCgCGCAAGGCCCGGACGGCTGtACTCACA-CAGCTAGCTCCATCTCCCTCAGCAGCACTAAGATTCCCACGTGACCAGGGCGACGGGCCTCAGCCAAACGTATCCTTGATATCTACTTAAGTCAAGGTTGACTCCGAACCCTATGGGTCGGT-GCCGTTAACAGGGAGTCTATATCTCGGCGTTCCATTGCTTGTTTCAAACTcCTGCTATAAGGTGAAAGCGCTGGAGGGCATAGT-TTATGCCCAAAGTTGCGCGTAGATCCGTCGGGATATG-TGCTATAATAAGGACTGC-TCGAG-GTAGGCGGTAACGG-CTCCCGCCTTCAGTaGGCGCGGAAC-TCGAATCGGAGTTAC-AG-GACTTGACCGA-GTCAT-ATCCAAGTTTATGTTACCCGATCGGATCCGGATGCTCGtATC-TGCGACGAGGTCGG-AAGACGGACGAAATACGATTCAACCGCGCG-AAC-CATTAGCATCTAACCTTTAGCCTCA-ATGGGTGTTAACGTGGTGGGCTCACTCGGCGTACTCTTTGTGCaACTATTC-CGTAT-GAACAACAG-TCAAGTTGCGACATGATGCTCTTACGTGATTCCCACAGTTTCCCACCTCAGGATGCTTTCTTTAGCT-AAA-CCCAATAGTTATGG-CGGCACCTT-CAGACTCCCACGAGGACGGCTATGACGTTGCTAAACCAtTCGCCGCCAAAGGCTAGCGCTAACGAGTTCTGTGAGTTTGTTCCGGGCCAGATCTCCAG-GATGGTCGCAACAACGCAGTACCGGT-TTTATACTGGTGACCCTCTACCTGTtATTAAGTTAcAGCGTTGTCCTACGTACATGGTCGTGAGTAC-TCGCGTAG-TCAAACGCCA--GG-ACTAGCAGCGAGAATTATTGTCGCGATACTTACTACAATAC-TTACCCGATATTGACGTGCAGGGTTGAAAGA-GATGG-ACAGTTGAATATC-TATTTTGACGGAATCCTCAAAACTCCCTCCACCTCAGGTaACGGCCCTGTCCGGGACCGCATTCTTGCATATATTG-GTtCCCAGAGCGTATCTAAGTTAG-TCTCTTGACCGTTCACCGACTC-TAGGGCGACTCGTTATCGCCCTCCGAAA-CGAT-GCTTtCGTTACCTCA-A-TGATGACAG-G-CTGTAACGTA-AGTGATCCCAATCTCACTCGTGCCTTGTCCACCGTTCCGTGAAGACGAAGCAATACGCGGAATACGTGGCTTCGTAATATTTTGACGATATGGGG-CTGGGACGC-TCAAGACTTCCATGACAAACAAAGTGAAGAGCAACTGCAT-CCCTCATCATGA-TCACTATTACCAGAG-TAGCGATGGAtAACGCTAATTTG-GTCAGGGCAGCTATCGCA-TCCCG-cAGGTGTAGGCG-G-AGACTTTTTCTTTTGTTGC-GAGTTGA-CA-GGTAATCTCACGGTATAAGCACGGTTATTTACG-CAAGCGACGTCCCTGGGAGaATCCGCCCACGTAGG-ACCCCATAATCCATAAAT-AC-TGCgGTCGAAACCTTCATATCGTGACAGAACCGCTTTC-TAGGGATG-CGGTCCCCGCATTCAGAGTTCT-ACTTTGGCCAGCGTG-AGACTTAACAACTCCACTTACGCGGTACATTGAAGT-C-GTTCAGTCCAGTGTGACCTGTGTAC-CGAATAACGTGTAGACCAGCGCGTCTACGACTTAGCGCGGCTCCACTCCA-a-AGCACCTTTTGGgACTTTC-CAACGAGC-CTGTTGGCCGTTAAGCGGTATTTCACAAATAGATCACCCTAGTGTCGGTAA-CCGACTACCCTATTGGGATCATCGTGAGCTCGAAACACTAGAGGCGGACCAACGGA--TGACATtTGATTCGGCTCTACAGAGCTTgTCGC-CAGAG-AAAAACTGTGGCAATCTACGCTCGCGGGG-AATTGACTTTAGCGGCCCCT-AGACAGGTGTGGGACACTAGTCTAGATTCACGTCCTACACGACATAACAGCACcTTCCTGGCCAGCCCAGAAATAGTACCTGGACGACATCCAGCCTTCCGACGCCATAATGT-GAGCCGTAGCGCCCACGACGATCAACGAGGAGAAATTTACAA-AGGCTGTGTGAATGCTACGTCGTCTACCATTGC-TCATCGAAACGAACGCAACGCACAGCATACAACGTT-TACCATGCCGGAGCGGGAT-CCTCAAGTACAGAA-AACAGAGGTCTAAACATGATCC-GAACAAATCGGTaGGTTTACACAGCTACCTC-GTC-CATTGGCGTACTGCATCGATCGTGCTTA--CTACGGTCATGCCGGCCCGCGATGCACGTACGAA-GGAATACCCTGTCTGCCCCCGCGCGAGTTACGCTGTCTCGCACATACCGAGCACT-GTCGTTCGAAGCTAAACTATGAGCCCAgCCGAGCTCCTTATGGCCGCAAC-GCtGGTGCGGCCAGCTGATAAATT-CCACAGtA-CACGATCCTCGTGTAAGATCTCG-GGCATAGTAAGTCA-TTTCACATGGTTAGGAGAGATAGAATACATGGTTCTGGTAGCTCAACCAGG-ATTTGTGGAACC-CTTGGCCCTTGGTGAGTGCTA-CAATAAAATTCTCCGTATGGGAC-AACCAAAGGGTGCTGGATGTGACTTCCCGGCCCAGGTTAGATGTCCATATCATTCATA-CATTGCCCGACCGACCCAATGCCTA-AATC-A-GA-GGCGCCTTAGCTAGTTCTTGtAGTGTGCCACGT-CCGGCCACGCAGACACGACCCT-CGGCGAGTGATCACCATTACC-GGATTGGCATCGAAGTCTTTTTCTGGGAAGTTAGCCAGTTtG-GTGTGCGGTG-CTTAGAATCT-TATTCCCA-GTCAAACGCCCCTGGGACGA-ATTGC-TAACCCTAGTT-GCCAC-gCCGGAACCATCTT-CGGGAGAG-TAGA-CA-A-ATCCGA-GTTAGATATGTTAGCGTCT-TCGTGAGTCTGAAATGTATCACTTCACCGC-AGAATA-CGCGAATGTCTGTTTGCCCTGGAC--TGACGGAaTTGGCTTAAAAGC-CGaCTAG-AGCATTTTGGTACGGT-TCCtATCC-GCGAT-GTAATTACCTATCTAGGTTATCGCTAG");
});
});
// only run the cabone_test_2 if it's in the URL someplace
if( document.location.href.indexOf('extended_tests=1') > -1 ) {
describe( 'BAM with carbone_test_2', function() {
var b;
beforeEach( function() {
b = new BAMStore({
browser: new Browser({ unitTestMode: true }),
bam: new XHRBlob('../../../data/carbone_test_2/RIB40_278_k51_cd_hit_est_sorted.bam'),
bai: new XHRBlob('../../../data/carbone_test_2/RIB40_278_k51_cd_hit_est_sorted.bam.bai'),
refSeq: { name: 'gi|338162049|dbj|BA000051.1|', start: 1, end: 5123684 }
});
});
it( 'loads some data', function() {
var loaded;
var features = [];
var done;
aspect.after( b, 'loadSuccess', function() {
loaded = true;
});
// need 2:3905491-4019507 NODE_423_length_210786_cov_16.121635 3919331 3979772
b.getFeatures({ start: 3799999, end: 4049999 },
function( feature ) {
features.push( feature );
},
function() {
done = true;
}
);
waitsFor( function() { return done; }, 2000 );
runs( function() {
expect(features.length).toEqual(13);
//console.log( distinctBins(features) );
});
});
});
}
});