From 06d776d796ebee8ed921df85855dd415d3170982 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 6 Sep 2017 17:22:01 -0700 Subject: [PATCH] Updated GA4GHAlignment from v0.5.1 to v0.6.0a10 --- src/main/GA4GHAlignment.js | 11 +- src/test/GA4GHAlignment-test.js | 78 ++++---- src/test/sources/GA4GHAlignmentSource-test.js | 12 +- test-data/README.md | 11 +- test-data/alignments.ga4gh.1.10000-11000.json | 1 + test-data/alignments.ga4gh.chr17.1-250.json | 180 +++++------------- 6 files changed, 110 insertions(+), 183 deletions(-) create mode 100644 test-data/alignments.ga4gh.1.10000-11000.json diff --git a/src/main/GA4GHAlignment.js b/src/main/GA4GHAlignment.js index a353e4fd..d3d8a7ed 100644 --- a/src/main/GA4GHAlignment.js +++ b/src/main/GA4GHAlignment.js @@ -10,7 +10,8 @@ import type {CigarOp, MateProperties, Strand} from './Alignment'; import ContigInterval from './ContigInterval'; import SamRead from './data/SamRead'; -// See https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/common.avdl +// See https://github.com/ga4gh/ga4gh-schemas/blob/master/src/main/proto/ga4gh/reads.proto +// Data can be queried at http://1kg.ga4gh.org/reads/search var OP_MAP = { ALIGNMENT_MATCH: 'M', INSERT: 'I', @@ -36,7 +37,7 @@ class GA4GHAlignment /* implements Alignment */ { _interval: ContigInterval; // alignment follows org.ga4gh.GAReadAlignment - // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl + // https://github.com/ga4gh/ga4gh-schemas/blob/master/src/main/proto/ga4gh/reads.proto constructor(alignment: Object) { this.alignment = alignment; this.pos = parseInt(alignment.alignment.position.position); @@ -56,7 +57,7 @@ class GA4GHAlignment /* implements Alignment */ { } getStrand(): Strand { - return this.alignment.alignment.position.reverseStrand ? '-' : '+'; + return this.alignment.alignment.position.strand == 'NEG_STRAND' ? '-' : '+'; } getQualityScores(): number[] { @@ -83,8 +84,8 @@ class GA4GHAlignment /* implements Alignment */ { var next = this.alignment.nextMatePosition; return next && { ref: next.referenceName, - pos: next.position, - strand: next.reverseStrand ? '-' : '+' + pos: parseInt(next.position), + strand: next.strand == 'NEG_STRAND' ? '-' : '+' }; } diff --git a/src/test/GA4GHAlignment-test.js b/src/test/GA4GHAlignment-test.js index e522821e..092d9b45 100644 --- a/src/test/GA4GHAlignment-test.js +++ b/src/test/GA4GHAlignment-test.js @@ -11,63 +11,69 @@ describe('GA4GHAlignment', function() { var sampleAlignments = []; before(function() { - return new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json').getAllString().then(data => { + return new RemoteFile('/test-data/alignments.ga4gh.1.10000-11000.json').getAllString().then(data => { sampleAlignments = JSON.parse(data).alignments; }); }); it('should read the sample alignments', function() { - expect(sampleAlignments).to.have.length(14); + expect(sampleAlignments).to.have.length(100); }); it('should provide basic accessors', function() { var a = new GA4GHAlignment(sampleAlignments[0]); - expect(a.name).to.equal('r000'); - expect(a.getSequence()).to.equal('ATTTAGCTAC'); - expect(a.getQualityScores()).to.deep.equal([32,32,32,32,32,32,32,32,32,32]); + expect(a.name).to.equal('ERR181329.21587964'); + expect(a.getSequence()).to.equal('ATAACCCTAACCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA'); + expect(a.getQualityScores()).to.deep.equal([2, 36, 36, 37, 37, 38, 37, 39, 37, 38, 38, 38, 3, 38, 38, 39, 38, 39, 39, 39, 38, 39, 39, 38, 40, 40, 38, 39, 39, 39, 39, 40, 38, 40, 39, 40, 38, 38, 38, 39, 38, 40, 37, 40, 38, 39, 39, 40, 40, 40, 39, 32, 39, 35, 39, 36, 38, 40, 39, 39, 39, 36, 39, 37, 39, 40, 39, 31, 39, 35, 36, 39, 37, 32, 40, 41, 38, 38, 37, 32, 39, 38, 38, 39, 33, 36, 25, 37, 38, 19, 35, 13, 37, 31, 35, 33, 34, 8, 33, 18]); expect(a.getStrand()).to.equal('+'); - expect(a.getInterval().toString()).to.equal('chr17:4-13'); // 0-based + expect(a.getInterval().toString()).to.equal('1:9999-10098'); // 0-based expect(a.cigarOps).to.deep.equal([ - {op: 'M', length: 10} + {op: 'M', length: 100} ]); expect(a.getMateProperties()).to.deep.equal({ - ref: 'chr17', - pos: 79, - strand: '+' + ref: '1', + pos: 10007, + strand: '-' }); }); it('should match SamRead', function() { var bam = new Bam(new RemoteFile('/test-data/chr17.1-250.bam')); - return bam.readAll().then(({alignments: samReads}) => { - // This is a workaround. See https://github.com/ga4gh/server/issues/488 - samReads.splice(-1, 1); + var json = new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json'); - expect(sampleAlignments.length).to.equal(samReads.length); - for (var i = 0; i < sampleAlignments.length; i++) { - var ga4gh = new GA4GHAlignment(sampleAlignments[i]), - bam = samReads[i]; - expect(ga4gh.getSequence()).to.equal(bam.getSequence()); - var interval = ga4gh.getInterval(); - expect(interval.start()).to.equal(bam.pos); + json.getAllString().then(data => { + var matchingBamAlignments = JSON.parse(data).alignments; - // See https://github.com/ga4gh/server/issues/491 - // expect(ga4gh.getStrand()).to.equal(bam.getStrand()); - // For the if statement, see https://github.com/ga4gh/server/issues/492 - var quality = ga4gh.getQualityScores(); - if (quality.length) { - expect(quality).to.deep.equal(bam.getQualityScores()); - } - expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps); - // After ga4gh#491, change this to a .deep.equal on getMateProperties() - var ga4ghMate = ga4gh.getMateProperties(), - bamMate = bam.getMateProperties(); - expect(!!ga4ghMate).to.equal(!!bamMate); - if (ga4ghMate && bamMate) { - expect(ga4ghMate.ref).to.equal(bamMate.ref); - expect(ga4ghMate.pos).to.equal(bamMate.pos); + return bam.readAll().then(({alignments: samReads}) => { + // This is a workaround. See https://github.com/ga4gh/server/issues/488 + samReads.splice(-1, 1); + + expect(matchingBamAlignments.length).to.equal(samReads.length); + for (var i = 0; i < matchingBamAlignments.length; i++) { + var ga4gh = new GA4GHAlignment(matchingBamAlignments[i]), + bam = samReads[i]; + expect(ga4gh.getSequence()).to.equal(bam.getSequence()); + var interval = ga4gh.getInterval(); + expect(interval.start()).to.equal(bam.pos); + + // See https://github.com/ga4gh/server/issues/491 + // expect(ga4gh.getStrand()).to.equal(bam.getStrand()); + // For the if statement, see https://github.com/ga4gh/server/issues/492 + var quality = ga4gh.getQualityScores(); + if (quality.length) { + expect(quality).to.deep.equal(bam.getQualityScores()); + } + expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps); + // After ga4gh#491, change this to a .deep.equal on getMateProperties() + var ga4ghMate = ga4gh.getMateProperties(), + bamMate = bam.getMateProperties(); + expect(!!ga4ghMate).to.equal(!!bamMate); + if (ga4ghMate && bamMate) { + expect(ga4ghMate.ref).to.equal(bamMate.ref); + expect(ga4ghMate.pos).to.equal(bamMate.pos); + } } - } + }); }); }); }); diff --git a/src/test/sources/GA4GHAlignmentSource-test.js b/src/test/sources/GA4GHAlignmentSource-test.js index b59e882d..c1a72d86 100644 --- a/src/test/sources/GA4GHAlignmentSource-test.js +++ b/src/test/sources/GA4GHAlignmentSource-test.js @@ -13,7 +13,7 @@ describe('GA4GHAlignmentSource', function() { var server: any = null, response; before(function () { - return new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json').getAllString().then(data => { + return new RemoteFile('/test-data/alignments.ga4gh.1.10000-11000.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); // _after_ we do a real XHR! }); @@ -24,16 +24,16 @@ describe('GA4GHAlignmentSource', function() { }); it('should fetch alignments from a server', function(done) { - server.respondWith('POST', '/v0.5.1/reads/search', + server.respondWith('POST', '/v0.6.0a10/reads/search', [200, { "Content-Type": "application/json" }, response]); var source = GA4GHAlignmentSource.create({ - endpoint: '/v0.5.1', + endpoint: '/v0.6.0a10', readGroupId: 'some-group-set:some-read-group', forcedReferenceId: null }); - var requestInterval = new ContigInterval('chr17', 10, 20); + var requestInterval = new ContigInterval('1', 10000, 10007); expect(source.getAlignmentsInRange(requestInterval)) .to.deep.equal([]); @@ -42,11 +42,11 @@ describe('GA4GHAlignmentSource', function() { source.on('networkdone', e => { progress.push('done'); }); source.on('newdata', () => { var reads = source.getAlignmentsInRange(requestInterval); - expect(reads).to.have.length(1); + expect(reads).to.have.length(16); done(); }); - source.rangeChanged({contig: 'chr17', start: 1, stop: 30}); + source.rangeChanged({contig: '1', start: 10000, stop: 10007}); server.respond(); }); diff --git a/test-data/README.md b/test-data/README.md index dbd82744..7ebe427f 100644 --- a/test-data/README.md +++ b/test-data/README.md @@ -62,9 +62,16 @@ corresponding SAM files for them in the same repo. This was hand-edited from the SAM equivalent of `test_input_1_a.bam` to have reads in chr17:1-250. It was then converted back to BAM/BAI using `samtools view`. -The JSON variant was formed by loading `chr17.1-250.bam` into v0.5.1 of the [GA4GH demo server][ga4gh] and querying for all the reads via: +The JSON variant was formed by loading `chr17.1-250.bam` into 0.6.0a10 of the [GA4GH demo server][ga4gh] and querying for all the reads via: - curl --data '{"readGroupIds":["pileup.js:chr17.1-250"]}' --header 'Content-Type: application/json' http://localhost:8000/v0.5.1/reads/search > alginments.ga4gh.chr17.1-250.json + curl --data '{"readGroupIds":["pileup.js:chr17.1-250"]}' --header 'Content-Type: application/json' http://localhost:8000/0.6.0a10/reads/search > alignments.ga4gh.chr17.1-250.json + + +#### alignments.ga4gh.1.10000-11000.json + +alignments.ga4gh.1.10000-11000.json was generated from the 0.6.0a10 GA4GH server http://1kgenomes.ga4gh.org/reads/search with the following +parameters: +{"readGroupIds": ["WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5Il0"], "referenceId": 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"fragmentLength": -379, "alignedSequence": "CTACCCCCAACCCTACCCCCACCCCTACCCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTATCCCTAACCCTAACCCTAACCCTAACCCTAA", "id": "WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5LjIwODQ0OTU0Il0", "alignment": {"position": {"position": "10338", "strand": "NEG_STRAND", "referenceName": "1"}, "cigar": [{"operation": "ALIGNMENT_MATCH", "operationLength": "15"}, {"operation": "INSERT", "operationLength": "1"}, {"operation": "ALIGNMENT_MATCH", "operationLength": "34"}, {"operation": "DELETE", "operationLength": "1"}, {"operation": "ALIGNMENT_MATCH", "operationLength": "8"}, {"operation": "DELETE", "operationLength": "1"}, {"operation": "ALIGNMENT_MATCH", "operationLength": "42"}], "mappingQuality": 29}, "nextMatePosition": {"position": "10059", "strand": "POS_STRAND", "referenceName": "1"}}]} diff --git a/test-data/alignments.ga4gh.chr17.1-250.json b/test-data/alignments.ga4gh.chr17.1-250.json index 4a96d55b..e9536f95 100644 --- a/test-data/alignments.ga4gh.chr17.1-250.json +++ b/test-data/alignments.ga4gh.chr17.1-250.json @@ -2,14 +2,7 @@ "nextPageToken": null, "alignments": [ { - "info": { - "RG": [ - "cow" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 32, @@ -26,10 +19,10 @@ "failedVendorQualityChecks": false, "fragmentName": "r000", "readNumber": 0, - "properPlacement": true, + "improperPlacement": true, "nextMatePosition": { "position": 79, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "supplementaryAlignment": false, @@ -41,7 +34,7 @@ "alignment": { "position": { "position": 4, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -56,14 +49,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "cow" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 32, @@ -80,10 +66,10 @@ "failedVendorQualityChecks": false, "fragmentName": "r000", "readNumber": 0, - "properPlacement": true, + "improperPlacement": false, "nextMatePosition": { "position": 49, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "supplementaryAlignment": false, @@ -95,7 +81,7 @@ "alignment": { "position": { "position": 19, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -110,7 +96,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { + "": { "YY": [ "100" ], @@ -129,10 +115,10 @@ "failedVendorQualityChecks": false, "fragmentName": "r001", "readNumber": 1, - "properPlacement": true, + "improperPlacement": true, "nextMatePosition": { "position": 36, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "supplementaryAlignment": false, @@ -144,7 +130,7 @@ "alignment": { "position": { "position": 24, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -179,23 +165,13 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "XB": [ - "-10" - ], - "XA": [ - "abc" - ], - "PG": [ - "colt" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [], "failedVendorQualityChecks": false, "fragmentName": "r002", "readNumber": null, - "properPlacement": false, + "improperPlacement": true, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -206,7 +182,7 @@ "alignment": { "position": { "position": 34, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -261,17 +237,13 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "cow" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [], "failedVendorQualityChecks": false, "fragmentName": "r003", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -282,7 +254,7 @@ "alignment": { "position": { "position": 44, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -302,20 +274,13 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "colt" - ], - "PG": [ - "colt" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [], "failedVendorQualityChecks": false, "fragmentName": "r004", "readNumber": null, - "properPlacement": false, + "improperPlacement": true, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -326,7 +291,7 @@ "alignment": { "position": { "position": 55, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -356,20 +321,13 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "cow" - ], - "PG": [ - "colt" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [], "failedVendorQualityChecks": false, "fragmentName": "r003", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -380,7 +338,7 @@ "alignment": { "position": { "position": 68, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -400,23 +358,16 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "fish" - ], - "PG": [ - "colt" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [], "failedVendorQualityChecks": false, "fragmentName": "r001", "readNumber": 0, - "properPlacement": true, + "improperPlacement": true, "nextMatePosition": { "position": 6, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "supplementaryAlignment": false, @@ -428,7 +379,7 @@ "alignment": { "position": { "position": 76, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -443,20 +394,13 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "colt" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [], "failedVendorQualityChecks": false, "fragmentName": "x1", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -467,7 +411,7 @@ "alignment": { "position": { "position": 79, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -482,14 +426,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "colt" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 30, @@ -517,7 +454,7 @@ "failedVendorQualityChecks": false, "fragmentName": "x2", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -528,7 +465,7 @@ "alignment": { "position": { "position": 90, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -543,14 +480,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "fish" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 30, @@ -583,7 +513,7 @@ "failedVendorQualityChecks": false, "fragmentName": "x3", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -594,7 +524,7 @@ "alignment": { "position": { "position": 103, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -619,14 +549,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "fish" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 30, @@ -658,7 +581,7 @@ "failedVendorQualityChecks": false, "fragmentName": "x4", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -669,7 +592,7 @@ "alignment": { "position": { "position": 114, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -684,14 +607,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "fish" - ], - "PG": [ - "bull" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 30, @@ -722,7 +638,7 @@ "failedVendorQualityChecks": false, "fragmentName": "x5", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -733,7 +649,7 @@ "alignment": { "position": { "position": 134, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [ @@ -748,11 +664,7 @@ "readGroupId": "pileup.js:chr17.1-250" }, { - "info": { - "RG": [ - "cow" - ] - }, + "attributes": {"attr": {"XC": {"values": [{"int32Value": 84}]}, "RG": {"values": [{"stringValue": "ERR181329"}]}}}, "duplicateFragment": false, "alignedQuality": [ 30, @@ -782,7 +694,7 @@ "failedVendorQualityChecks": false, "fragmentName": "x6", "readNumber": null, - "properPlacement": false, + "improperPlacement": false, "nextMatePosition": null, "supplementaryAlignment": false, "numberReads": null, @@ -793,7 +705,7 @@ "alignment": { "position": { "position": 164, - "reverseStrand": false, + "strand": "POS_STRAND", "referenceName": "chr17" }, "cigar": [