@gmod/cram 1.6.3 → 1.6.4

package/CHANGELOG.md

@@ -1,3 +1,7 @@
+# v1.6.4
+
+- Fix off by one in returning features from getRecordsFromRange
+
 # v1.6.3
 
 - Optimize CRAM parsing slightly (15% improvement on many short reads). This removes support for big endian machines

package/dist/craiIndex.js

@@ -196,7 +196,7 @@ var CraiIndex = /** @class */ (function () {
                         compare = function (entry) {
                             var entryStart = entry.start;
                             var entryEnd = entry.start + entry.span;
-                            if (entryStart >= queryEnd) {
+                            if (entryStart > queryEnd) {
                                 return -1;
                             } // entry is ahead of query
                             if (entryEnd <= queryStart) {

package/dist/craiIndex.js.map

@@ -1 +1 @@
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package/dist/cram-bundle.js

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  * @license  MIT
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0!==n.mateRecordNumber&&n.mateRecordNumber!==e);r.readName||(r.readName=String(r.uniqueId),n.readName=r.readName),r.mate={sequenceId:n.sequenceId,alignmentStart:n.alignmentStart,uniqueId:n.uniqueId},n.readName&&(r.mate.readName=n.readName),n.mate||void 0!==n.mateRecordNumber||(n.mate={sequenceId:r.sequenceId,alignmentStart:r.alignmentStart,uniqueId:r.uniqueId},r.readName&&(n.mate.readName=r.readName)),r.flags|=f.default.BAM_FPAIRED,n.flags&f.default.BAM_FUNMAP&&(r.flags|=f.default.BAM_FMUNMAP),r.flags&f.default.BAM_FUNMAP&&(n.flags|=f.default.BAM_FMUNMAP),n.flags&f.default.BAM_FREVERSE&&(r.flags|=f.default.BAM_FMREVERSE),r.flags&f.default.BAM_FREVERSE&&(n.flags|=f.default.BAM_FMREVERSE),void 0===r.templateLength&&(i?function(t,e,r){var n=function e(r){var n=[r];if(r.mateRecordNumber>=0){var i=t[r.mateRecordNumber];if(!i)throw new a.CramMalformedError("intra-slice mate record not found, this file seems malformed");n.push.apply(n,e(i))}return n}(r),i=n.map((function(t){return t.alignmentStart})),o=n.map((function(t){return t.alignmentStart+t.readLength-1})),s=Math.max.apply(Math,o)-Math.min.apply(Math,i)+1;s>=0&&n.forEach((function(t){if(void 0!==t.templateLength)throw new a.CramMalformedError("mate pair group has some members that have template lengths already, this file seems malformed");t.templateLength=s}))}(t,0,r):function(t,e){var r=Math.min(t.alignmentStart,e.alignmentStart),n=Math.max(t.alignmentStart+t.readLength-1,e.alignmentStart+e.readLength-1)-r+1;t.templateLength=n,e.templateLength=n}(r,n)),delete r.mateRecordNumber}var h=function(){function t(t,e){this.container=t,this.file=t.file,this.containerPosition=e}return t.prototype.getHeader=function(){return n(this,void 0,void 0,(function(){var t,e,r;return i(this,(function(n){switch(n.label){case 0:return[4,this.file.getSectionParsers()];case 1:return t=n.sent(),[4,this.container.getHeader()];case 2:return e=n.sent(),[4,this.file.readBlock(e._endPosition+this.containerPosition)];case 3:if("MAPPED_SLICE_HEADER"===(r=n.sent()).contentType)r.content=(0,s.parseItem)(r.content,t.cramMappedSliceHeader.parser,0,e._endPosition);else{if("UNMAPPED_SLICE_HEADER"!==r.contentType)throw new a.CramMalformedError("error reading slice header block, invalid content type ".concat(r._contentType));r.content=(0,s.parseItem)(r.content,t.cramUnmappedSliceHeader.parser,0,e._endPosition)}return[2,r]}}))}))},t.prototype.getBlocks=function(){return n(this,void 0,void 0,(function(){var t,e,r,n,o,a;return i(this,(function(i){switch(i.label){case 0:return[4,this.getHeader()];case 1:t=i.sent(),e=t._endPosition,r=new Array(t.content.numBlocks),n=0,i.label=2;case 2:return n<r.length?(o=r,a=n,[4,this.file.readBlock(e)]):[3,5];case 3:o[a]=i.sent(),e=r[n]._endPosition,i.label=4;case 4:return n+=1,[3,2];case 5:return[2,r]}}))}))},t.prototype.getCoreDataBlock=function(){return n(this,void 0,void 0,(function(){return i(this,(function(t){switch(t.label){case 0:return[4,this.getBlocks()];case 1:return[2,t.sent()[0]]}}))}))},t.prototype._getBlocksContentIdIndex=function(){return n(this,void 0,void 0,(function(){var t,e;return i(this,(function(r){switch(r.label){case 0:return[4,this.getBlocks()];case 1:return t=r.sent(),e={},t.forEach((function(t){"EXTERNAL_DATA"===t.contentType&&(e[t.contentId]=t)})),[2,e]}}))}))},t.prototype.getBlockByContentId=function(t){return n(this,void 0,void 0,(function(){return i(this,(function(e){switch(e.label){case 0:return[4,this._getBlocksContentIdIndex()];case 1:return[2,e.sent()[t]]}}))}))},t.prototype.getReferenceRegion=function(){return n(this,void 0,void 0,(function(){var t,e,r,n;return i(this,(function(i){switch(i.label){case 0:return[4,this.getHeader()];case 1:return(t=i.sent().content).refSeqId<0?[2,void 0]:[4,this.container.getCompressionScheme()];case 2:if(e=i.sent(),t.refBaseBlockId>=0){if(!(r=this.getBlockByContentId(t.refBaseBlockId)))throw new a.CramMalformedError("embedded reference specified, but reference block does not exist");if(t.span>r.uncompressedSize)throw new a.CramMalformedError("Embedded reference is too small");return[2,{seq:r.data.toString("utf8"),start:t.refSeqStart,end:t.refSeqStart+t.refSeqSpan-1,span:t.refSeqSpan}]}if(!e.referenceRequired&&!this.file.fetchReferenceSequenceCallback)return[3,4];if(!this.file.fetchReferenceSequenceCallback)throw new Error("reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence");return[4,this.file.fetchReferenceSequenceCallback(t.refSeqId,t.refSeqStart,t.refSeqStart+t.refSeqSpan-1)];case 3:if((n=i.sent()).length!==t.refSeqSpan)throw new a.CramArgumentError("seqFetch callback returned a reference sequence of the wrong length");return[2,{seq:n,start:t.refSeqStart,end:t.refSeqStart+t.refSeqSpan-1,span:t.refSeqSpan}];case 4:return[2,void 0]}}))}))},t.prototype.getAllRecords=function(){return this.getRecords((function(){return!0}))},t.prototype._fetchRecords=function(){return n(this,void 0,void 0,(function(){var t,e,r,n,o,f,h,l,d,p,g,y,v,m,b,_,w=this;return i(this,(function(i){switch(i.label){case 0:return[4,this.file.getDefinition()];case 1:return t=i.sent().majorVersion,[4,this.container.getCompressionScheme()];case 2:return e=i.sent(),[4,this.getHeader()];case 3:return r=i.sent(),[4,this._getBlocksContentIdIndex()];case 4:return n=i.sent(),t>1&&this.file.options.checkSequenceMD5&&r.content.refSeqId>=0&&"0000000000000000"!==r.content.md5.join("")?[4,this.getReferenceRegion()]:[3,6];case 5:if((o=i.sent())&&(f=o.seq,h=o.start,l=o.end,d=(0,s.sequenceMD5)(f),p=r.content.md5.map((function(t){return(t<16?"0":"")+t.toString(16)})).join(""),d!==p))throw new a.CramMalformedError("MD5 checksum reference mismatch for ref ".concat(r.content.refSeqId," pos ").concat(h,"..").concat(l,". recorded MD5: ").concat(p,", calculated MD5: ").concat(d));i.label=6;case 6:return[4,this.getCoreDataBlock()];case 7:for(g=i.sent(),y={lastAlignmentStart:r.content.refSeqStart||0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor:function(t){var e=this.map.get(t);return void 0===e&&(e={bitPosition:7,bytePosition:0},this.map.set(t,e)),e}}},v=function(t){var r=e.getCodecForDataSeries(t);if(!r)throw new a.CramMalformedError("no codec defined for ".concat(t," data series"));return r.decode(w,g,n,y)},m=new Array(r.content.numRecords),b=0;b<m.length;b+=1)try{m[b]=(0,u.default)(this,v,e,r,g,n,y,t,b),m[b].uniqueId=r.contentPosition+r.content.recordCounter+b+1}catch(t){if(t instanceof a.CramBufferOverrunError){console.warn("read attempted beyond end of buffer, file seems truncated."),m=m.filter((function(t){return!!t}));break}throw t}for(b=0;b<m.length;b+=1)(_=m[b].mateRecordNumber)>=0&&c(m,b,m[b],m[_]);return[2,m]}}))}))},t.prototype.getRecords=function(t){return n(this,void 0,void 0,(function(){var e,r,o,a,s,f,u,c,h,l,d,p=this;return i(this,(function(g){switch(g.label){case 0:return e=this.container.filePosition+this.containerPosition,(r=this.file.featureCache.get(e))||(r=this._fetchRecords(),this.file.featureCache.set(e,r)),[4,r];case 1:return(o=g.sent().filter(t)).length&&this.file.fetchReferenceSequenceCallback?[4,this.getHeader()]:[3,5];case 2:return(a=g.sent()).content.refSeqId>=0||-2===a.content.refSeqId?(s=a.content.refSeqId>=0?a.content.refSeqId:void 0,[4,this.container.getCompressionScheme()]):[3,5];case 3:for(f=g.sent(),u={},h=0;h<o.length;h+=1)l=void 0!==s?s:o[h].sequenceId,(d=u[l])||(d={id:l,start:o[h].alignmentStart,end:-1/0},u[l]=d),(c=o[h].alignmentStart+(o[h].lengthOnRef||o[h].readLength)-1)>d.end&&(d.end=c),o[h].alignmentStart<d.start&&(d.start=o[h].alignmentStart);return[4,Promise.all(Object.values(u).map((function(t){return n(p,void 0,void 0,(function(){var e;return i(this,(function(r){switch(r.label){case 0:return-1!==t.id&&t.start<=t.end?(e=t,[4,this.file.fetchReferenceSequenceCallback(t.id,t.start,t.end)]):[3,2];case 1:e.seq=r.sent(),r.label=2;case 2:return[2]}}))}))})))];case 4:for(g.sent(),h=0;h<o.length;h+=1)l=void 0!==s?s:o[h].sequenceId,(d=u[l])&&d.seq&&o[h].addReferenceSequence(d,f);g.label=5;case 5:return[2,o]}}))}))},t}();e.default=h,"getHeader getBlocks _getBlocksContentIdIndex".split(" ").forEach((function(t){return(0,s.tinyMemoize)(h,t)}))},function(t,e,r){"use strict";var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var i=n(r(23)),o=r(0),a=n(r(66)),s=n(r(12));function f(t){for(var e="",r=0;r<t.length&&0!==t[r];r++)e+=String.fromCharCode(t[r]);return e}function u(t,e){if("Z"===t)return f(e);if("A"===t)return String.fromCharCode(e[0]);if("I"===t)return i.default.fromBytesLE(e).toNumber();if("i"===t)return new Int32Array(e.buffer)[0];if("s"===t)return new Int16Array(e.buffer)[0];if("S"===t)return new Uint16Array(e.buffer)[0];if("c"===t)return new Int8Array(e.buffer)[0];if("C"===t)return e[0];if("f"===t)return new Float32Array(e.buffer)[0];if("H"===t)return Number.parseInt(f(e).replace(/^0x/,""),16);if("B"===t)return function(t){var e=String.fromCharCode(t[0]),r=Int32Array.from(t.slice(1))[0],n=new Array(r);if(t=t.slice(5),"c"===e)for(var i=new Int8Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("C"===e)for(i=new Uint8Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("s"===e)for(i=new Int16Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("S"===e)for(i=new Uint16Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("i"===e)for(i=new Int32Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("I"===e)for(i=new Uint32Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else{if("f"!==e)throw new Error("unknown type: "+e);for(i=new Float32Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o]}return n}(e);throw new o.CramMalformedError("Unrecognized tag type ".concat(t))}e.default=function(t,e,r,n,i,c,h,l,d){var p=new a.default;if(p.flags=e("BF"),p.cramFlags=e("CF"),l>1&&-2===n.content.refSeqId?p.sequenceId=e("RI"):p.sequenceId=n.content.refSeqId,p.readLength=e("RL"),p.alignmentStart=e("AP"),r.APdelta&&(p.alignmentStart+=h.lastAlignmentStart),h.lastAlignmentStart=p.alignmentStart,p.readGroupId=e("RG"),r.readNamesIncluded&&(p.readName=f(e("RN"))),p.isDetached()){var g={};g.flags=e("MF"),r.readNamesIncluded||(g.readName=f(e("RN")),p.readName=g.readName),g.sequenceId=e("NS"),g.alignmentStart=e("NP"),(g.flags||g.sequenceId>-1)&&(p.mate=g),p.templateSize=e("TS"),g.flags&s.default.CRAM_M_UNMAP&&(p.flags|=s.default.BAM_FMUNMAP),g.flags&s.default.CRAM_M_REVERSE&&(p.flags|=s.default.BAM_FMREVERSE)}else p.hasMateDownStream()&&(p.mateRecordNumber=e("NF")+d+1);var y=e("TL");if(y<0)throw new o.CramMalformedError("invalid TL index");for(var v=r.getTagNames(y),m=v.length,b=0;b<m;b+=1){var _=v[b],w=_.substr(0,2),A=_.substr(2,1),S=r.getCodecForTag(_);if(!S)throw new o.CramMalformedError("no codec defined for auxiliary tag ".concat(_));var E=S.decode(t,i,c,h);p.tags[w]=u(A,E)}if(p.isSegmentUnmapped())if(p.isUnknownBases())p.readBases=null,p.qualityScores=null;else{for(k=new Array(p.readLength),b=0;b<k.length;b+=1)k[b]=e("BA");if(p.readBases=String.fromCharCode.apply(String,k),p.isPreservingQualityScores()){for(b=0;b<k.length;b+=1)k[b]=e("QS");p.qualityScores=k}}else{var C=e("FN");C&&(p.readFeatures=function(t,e,r,n,i){var a=0,s=t.alignmentStart-1,f=new Array(e);function u(t){var e=t[0],n=t[1],i=r(n);return"character"===e?String.fromCharCode(i):"string"===e?i.toString("utf8"):"numArray"===e?i.toArray():i}for(var c=0;c<e;c+=1){var h=String.fromCharCode(r("FC")),l=r("FP"),d={code:h},p={B:["character","BA"],S:["string",i>1?"SC":"IN"],X:["number","BS"],D:["number","DL"],I:["string","IN"],i:["character","BA"],b:["string","BB"],q:["numArray","QQ"],Q:["number","QS"],H:["number","HC"],P:["number","PD"],N:["number","RS"]}[h];if(!p)throw new o.CramMalformedError('invalid read feature code 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t.prototype.isPaired=function(){return!!(this.flags&i.default.BAM_FPAIRED)},t.prototype.isProperlyPaired=function(){return!!(this.flags&i.default.BAM_FPROPER_PAIR)},t.prototype.isSegmentUnmapped=function(){return!!(this.flags&i.default.BAM_FUNMAP)},t.prototype.isMateUnmapped=function(){return!!(this.flags&i.default.BAM_FMUNMAP)},t.prototype.isReverseComplemented=function(){return!!(this.flags&i.default.BAM_FREVERSE)},t.prototype.isMateReverseComplemented=function(){return!!(this.flags&i.default.BAM_FMREVERSE)},t.prototype.isRead1=function(){return!!(this.flags&i.default.BAM_FREAD1)},t.prototype.isRead2=function(){return!!(this.flags&i.default.BAM_FREAD2)},t.prototype.isSecondary=function(){return!!(this.flags&i.default.BAM_FSECONDARY)},t.prototype.isFailedQc=function(){return!!(this.flags&i.default.BAM_FQCFAIL)},t.prototype.isDuplicate=function(){return!!(this.flags&i.default.BAM_FDUP)},t.prototype.isSupplementary=function(){return!!(this.flags&i.default.BAM_FSUPPLEMENTARY)},t.prototype.isDetached=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_DETACHED)},t.prototype.hasMateDownStream=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_MATE_DOWNSTREAM)},t.prototype.isPreservingQualityScores=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)},t.prototype.isUnknownBases=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_NO_SEQ)},t.prototype.getReadBases=function(){return!this.readBases&&this._refRegion&&(this.readBases=function(t,e){if((t.lengthOnRef||t.readLength)&&!t.isUnknownBases()){var r=t.alignmentStart-e.start;if(!t.readFeatures)return e.seq.substr(r,t.lengthOnRef).toUpperCase();for(var n="",i=r,o=0;n.length<t.readLength;)if(o<t.readFeatures.length){var a=t.readFeatures[o];if("Q"===a.code||"q"===a.code)o+=1;else if(a.pos===n.length+1)if(o+=1,"b"===a.code){var s=a.data.split(","),f=String.fromCharCode.apply(String,s);n+=f,i+=f.length}else"B"===a.code?(n+=a.data[0],i+=1):"X"===a.code?(n+=a.sub,i+=1):"I"===a.code?n+=a.data:"D"===a.code?i+=a.data:"i"===a.code?n+=a.data:"N"===a.code?i+=a.data:"S"===a.code?n+=a.data:"P"===a.code||a.code;else if(o<t.readFeatures.length){n+=u=e.seq.substr(i,t.readFeatures[o].pos-n.length-1),i+=u.length}}else{var u;n+=u=e.seq.substr(i,t.readLength-n.length),i+=u.length}return n.toUpperCase()}}(this,this._refRegion)),this.readBases},t.prototype.getPairOrientation=function(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){var t=this.isReverseComplemented()?"R":"F",e=this.isMateReverseComplemented()?"R":"F",r=" ",n=" ";this.isRead1()?(r="1",n="2"):this.isRead2()&&(r="2",n="1");var i=[],o=this.templateLength||this.templateSize;return this.alignmentStart>this.mate.alignmentStart&&o>0&&(o=-o),o>0?(i[0]=t,i[1]=r,i[2]=e,i[3]=n):(i[2]=t,i[3]=r,i[0]=e,i[1]=n),i.join("")}return null},t.prototype.addReferenceSequence=function(t,e){this.readFeatures&&this.readFeatures.forEach((function(r){"X"===r.code&&function(t,e,r,n){if(e){var i=n.refPos-e.start,a=e.seq.charAt(i);a&&(n.ref=a);var s=o[a];void 0===s&&(s=4);var f=r.substitutionMatrix[s][n.data];f&&(n.sub=f)}}(0,t,e,r)})),!this.readBases&&t.start<=this.alignmentStart&&t.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=t)},t.prototype.toJSON=function(){var t=this,e={};return Object.keys(this).forEach((function(r){"_"!==r.charAt(0)&&(e[r]=t[r])})),e.readBases=this.getReadBases(),e},t}();e.default=a},function(t,e,r){"use 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e[0][t[0]>>6&3]="C",e[0][t[0]>>4&3]="G",e[0][t[0]>>2&3]="T",e[0][t[0]>>0&3]="N",e[1][t[1]>>6&3]="A",e[1][t[1]>>4&3]="G",e[1][t[1]>>2&3]="T",e[1][t[1]>>0&3]="N",e[2][t[2]>>6&3]="A",e[2][t[2]>>4&3]="C",e[2][t[2]>>2&3]="T",e[2][t[2]>>0&3]="N",e[3][t[3]>>6&3]="A",e[3][t[3]>>4&3]="C",e[3][t[3]>>2&3]="G",e[3][t[3]>>0&3]="N",e[4][t[4]>>6&3]="A",e[4][t[4]>>4&3]="C",e[4][t[4]>>2&3]="G",e[4][t[4]>>0&3]="T",e}(t.preservation.SM),this.dataSeriesCodecCache=new Map,this.tagCodecCache={}}return t.prototype.getCodecForTag=function(t){if(!this.tagCodecCache[t]){var e=this.tagEncoding[t];e&&(this.tagCodecCache[t]=(0,i.instantiateCodec)(e,"byteArray"))}return this.tagCodecCache[t]},t.prototype.getTagNames=function(t){return this.tagIdsDictionary[t]},t.prototype.getCodecForDataSeries=function(t){var e=this.dataSeriesCodecCache.get(t);if(void 0===e){var r=this.dataSeriesEncoding[t];if(r){var a=o[t];if(!a)throw new n.CramMalformedError("data series name ".concat(t," not defined in file compression header"));e=(0,i.instantiateCodec)(r,a),this.dataSeriesCodecCache.set(t,e)}}return e},t.prototype.toJSON=function(){var t=this,e={};return Object.keys(this).forEach((function(r){/Cache$/.test(r)||(e[r]=t[r])})),e},t}();e.default=a},function(t,e,r){"use strict";var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0}),e.instantiateCodec=e.getCodecClassWithId=void 0;var i=r(0),o=n(r(69)),a=n(r(70)),s=n(r(71)),f=n(r(72)),u=n(r(73)),c=n(r(74)),h=n(r(75)),l={1:a.default,3:o.default,4:f.default,5:s.default,6:u.default,7:h.default,9:c.default};function d(t){return l[t]}e.getCodecClassWithId=d,e.instantiateCodec=function t(e,r){var n=d("ignore"===r?0:e.codecId);if(!n)throw new i.CramUnimplementedError("no codec implemented for codec ID ".concat(e.codecId));return new n(e.parameters,r,t)}},function(t,e,r){"use strict";var n,i=this&&this.__extends||(n=function(t,e){return(n=Object.setPrototypeOf||{__proto__:[]}instanceof 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Array(this.parameters.numCodes),r=0;r<this.parameters.numCodes;r+=1)e[r]={symbol:this.parameters.symbols[r],bitLength:this.parameters.bitLengths[r]};e=e.sort((function(t,e){return t.bitLength-e.bitLength||t.symbol-e.symbol})),this.codeBook={},e.forEach((function(e){t.codeBook[e.bitLength]||(t.codeBook[e.bitLength]=[]),t.codeBook[e.bitLength].push(e.symbol)}))},e.prototype.buildCodes=function(){var t=this;this.codes={};var e=0,r=-1;Object.entries(this.codeBook).forEach((function(n){var i=n[0],o=n[1];i=parseInt(i,10),o.forEach((function(n){var o={bitLength:i,value:n};r+=1;var s,f,u=i-e;if(r<<=u,o.bitCode=r,e+=u,16843009*((f=(858993459&(f=(s=r)-(s>>1)&1431655765))+(f>>2&858993459))+(f>>4)&252645135)>>24>i)throw new a.CramMalformedError("Symbol out of range");t.codes[n]=o}))}))},e.prototype.buildCaches=function(){this.sortedCodes=Object.values(this.codes).sort((function(t,e){return t.bitLength-e.bitLength||t.bitCode-e.bitCode})),this.sortedByValue=Object.values(this.codes).sort((function(t,e){return t.value-e.value})),this.sortedValuesByBitCode=this.sortedCodes.map((function(t){return t.value})),this.sortedBitCodes=this.sortedCodes.map((function(t){return t.bitCode})),this.sortedBitLengthsByBitCode=this.sortedCodes.map((function(t){return t.bitLength}));var t=Math.max.apply(Math,this.sortedBitCodes);this.bitCodeToValue=new Array(t+1).fill(-1);for(var e=0;e<this.sortedBitCodes.length;e+=1)this.bitCodeToValue[this.sortedCodes[e].bitCode]=e},e.prototype.decode=function(t,e,r,n){return this._decode(t,e,n.coreBlock)},e.prototype._decodeZeroLengthCode=function(){return this.sortedCodes[0].value},e.prototype._decode=function(t,e,r){for(var n=e.content,i=0,o=0,s=0;s<this.sortedCodes.length;s+=1){var f=this.sortedCodes[s].bitLength;o<<=f-i,o|=this._getBits(n,r,f-i),i=f;var u=this.bitCodeToValue[o];if(u>-1&&this.sortedBitLengthsByBitCode[u]===f)return this.sortedValuesByBitCode[u];for(var c=s;this.sortedCodes[c+1].bitLength===f&&c<this.sortedCodes.length;c+=1)s+=1}throw new a.CramMalformedError("Huffman symbol not found.")},e}(o(r(3)).default);e.default=s},function(t,e,r){"use strict";var n,i=this&&this.__extends||(n=function(t,e){return(n=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&(t[r]=e[r])})(t,e)},function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");function r(){this.constructor=t}n(t,e),t.prototype=null===e?Object.create(e):(r.prototype=e.prototype,new r)}),o=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var a=r(0),s=o(r(3)),f=r(5),u=function(t){function e(e,r){void 0===e&&(e={});var 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e[0];if("f"===t)return new Float32Array(e.buffer)[0];if("H"===t)return Number.parseInt(f(e).replace(/^0x/,""),16);if("B"===t)return function(t){var e=String.fromCharCode(t[0]),r=Int32Array.from(t.slice(1))[0],n=new Array(r);if(t=t.slice(5),"c"===e)for(var i=new Int8Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("C"===e)for(i=new Uint8Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("s"===e)for(i=new Int16Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("S"===e)for(i=new Uint16Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("i"===e)for(i=new Int32Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else if("I"===e)for(i=new Uint32Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o];else{if("f"!==e)throw new Error("unknown type: "+e);for(i=new Float32Array(t.buffer),o=0;o<r;o+=1)n[o]=i[o]}return n}(e);throw new o.CramMalformedError("Unrecognized tag type ".concat(t))}e.default=function(t,e,r,n,i,c,h,l,d){var p=new a.default;if(p.flags=e("BF"),p.cramFlags=e("CF"),l>1&&-2===n.content.refSeqId?p.sequenceId=e("RI"):p.sequenceId=n.content.refSeqId,p.readLength=e("RL"),p.alignmentStart=e("AP"),r.APdelta&&(p.alignmentStart+=h.lastAlignmentStart),h.lastAlignmentStart=p.alignmentStart,p.readGroupId=e("RG"),r.readNamesIncluded&&(p.readName=f(e("RN"))),p.isDetached()){var g={};g.flags=e("MF"),r.readNamesIncluded||(g.readName=f(e("RN")),p.readName=g.readName),g.sequenceId=e("NS"),g.alignmentStart=e("NP"),(g.flags||g.sequenceId>-1)&&(p.mate=g),p.templateSize=e("TS"),g.flags&s.default.CRAM_M_UNMAP&&(p.flags|=s.default.BAM_FMUNMAP),g.flags&s.default.CRAM_M_REVERSE&&(p.flags|=s.default.BAM_FMREVERSE)}else p.hasMateDownStream()&&(p.mateRecordNumber=e("NF")+d+1);var y=e("TL");if(y<0)throw new o.CramMalformedError("invalid TL index");for(var v=r.getTagNames(y),m=v.length,b=0;b<m;b+=1){var _=v[b],w=_.substr(0,2),A=_.substr(2,1),S=r.getCodecForTag(_);if(!S)throw new o.CramMalformedError("no codec defined for auxiliary tag ".concat(_));var E=S.decode(t,i,c,h);p.tags[w]=u(A,E)}if(p.isSegmentUnmapped())if(p.isUnknownBases())p.readBases=null,p.qualityScores=null;else{for(k=new Array(p.readLength),b=0;b<k.length;b+=1)k[b]=e("BA");if(p.readBases=String.fromCharCode.apply(String,k),p.isPreservingQualityScores()){for(b=0;b<k.length;b+=1)k[b]=e("QS");p.qualityScores=k}}else{var C=e("FN");C&&(p.readFeatures=function(t,e,r,n,i){var a=0,s=t.alignmentStart-1,f=new Array(e);function u(t){var e=t[0],n=t[1],i=r(n);return"character"===e?String.fromCharCode(i):"string"===e?i.toString("utf8"):"numArray"===e?i.toArray():i}for(var c=0;c<e;c+=1){var h=String.fromCharCode(r("FC")),l=r("FP"),d={code:h},p={B:["character","BA"],S:["string",i>1?"SC":"IN"],X:["number","BS"],D:["number","DL"],I:["string","IN"],i:["character","BA"],b:["string","BB"],q:["numArray","QQ"],Q:["number","QS"],H:["number","HC"],P:["number","PD"],N:["number","RS"]}[h];if(!p)throw new o.CramMalformedError('invalid read feature code "'.concat(h,'"'));d.data=u(p);var g={B:["number","QS"]}[h];g&&(d.data=[d.data,u(g)]),a+=l,d.pos=a,s+=l,d.refPos=s,"D"===h||"N"===h?s+=d.data:"I"===h||"S"===h?s-=d.data.length:"i"===h&&(s-=1),f[c]=d}return f}(p,C,e,0,l));var B=p.readLength;if(p.readFeatures&&p.readFeatures.forEach((function(t){var e=t.code,r=t.data;"D"===e||"N"===e?B+=r:"I"===e||"S"===e?B-=r.length:"i"===e&&(B-=1)})),Number.isNaN(B)&&(console.warn("".concat(p.readName||"".concat(p.sequenceId,":").concat(p.alignmentStart)," record has invalid read features")),B=p.readLength),p.lengthOnRef=B,p.mappingQuality=e("MQ"),p.isPreservingQualityScores()){for(var k=new Array(p.readLength),b=0;b<k.length;b+=1)k[b]=e("QS");p.qualityScores=k}}return p}},function(t,e,r){"use strict";var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var i=n(r(12));var o={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};var a=function(){function t(){this.tags={}}return t.prototype.isPaired=function(){return!!(this.flags&i.default.BAM_FPAIRED)},t.prototype.isProperlyPaired=function(){return!!(this.flags&i.default.BAM_FPROPER_PAIR)},t.prototype.isSegmentUnmapped=function(){return!!(this.flags&i.default.BAM_FUNMAP)},t.prototype.isMateUnmapped=function(){return!!(this.flags&i.default.BAM_FMUNMAP)},t.prototype.isReverseComplemented=function(){return!!(this.flags&i.default.BAM_FREVERSE)},t.prototype.isMateReverseComplemented=function(){return!!(this.flags&i.default.BAM_FMREVERSE)},t.prototype.isRead1=function(){return!!(this.flags&i.default.BAM_FREAD1)},t.prototype.isRead2=function(){return!!(this.flags&i.default.BAM_FREAD2)},t.prototype.isSecondary=function(){return!!(this.flags&i.default.BAM_FSECONDARY)},t.prototype.isFailedQc=function(){return!!(this.flags&i.default.BAM_FQCFAIL)},t.prototype.isDuplicate=function(){return!!(this.flags&i.default.BAM_FDUP)},t.prototype.isSupplementary=function(){return!!(this.flags&i.default.BAM_FSUPPLEMENTARY)},t.prototype.isDetached=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_DETACHED)},t.prototype.hasMateDownStream=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_MATE_DOWNSTREAM)},t.prototype.isPreservingQualityScores=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)},t.prototype.isUnknownBases=function(){return!!(this.cramFlags&i.default.CRAM_FLAG_NO_SEQ)},t.prototype.getReadBases=function(){return!this.readBases&&this._refRegion&&(this.readBases=function(t,e){if((t.lengthOnRef||t.readLength)&&!t.isUnknownBases()){var r=t.alignmentStart-e.start;if(!t.readFeatures)return e.seq.substr(r,t.lengthOnRef).toUpperCase();for(var n="",i=r,o=0;n.length<t.readLength;)if(o<t.readFeatures.length){var a=t.readFeatures[o];if("Q"===a.code||"q"===a.code)o+=1;else if(a.pos===n.length+1)if(o+=1,"b"===a.code){var s=a.data.split(","),f=String.fromCharCode.apply(String,s);n+=f,i+=f.length}else"B"===a.code?(n+=a.data[0],i+=1):"X"===a.code?(n+=a.sub,i+=1):"I"===a.code?n+=a.data:"D"===a.code?i+=a.data:"i"===a.code?n+=a.data:"N"===a.code?i+=a.data:"S"===a.code?n+=a.data:"P"===a.code||a.code;else if(o<t.readFeatures.length){n+=u=e.seq.substr(i,t.readFeatures[o].pos-n.length-1),i+=u.length}}else{var u;n+=u=e.seq.substr(i,t.readLength-n.length),i+=u.length}return n.toUpperCase()}}(this,this._refRegion)),this.readBases},t.prototype.getPairOrientation=function(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){var t=this.isReverseComplemented()?"R":"F",e=this.isMateReverseComplemented()?"R":"F",r=" ",n=" ";this.isRead1()?(r="1",n="2"):this.isRead2()&&(r="2",n="1");var i=[],o=this.templateLength||this.templateSize;return this.alignmentStart>this.mate.alignmentStart&&o>0&&(o=-o),o>0?(i[0]=t,i[1]=r,i[2]=e,i[3]=n):(i[2]=t,i[3]=r,i[0]=e,i[1]=n),i.join("")}return null},t.prototype.addReferenceSequence=function(t,e){this.readFeatures&&this.readFeatures.forEach((function(r){"X"===r.code&&function(t,e,r,n){if(e){var i=n.refPos-e.start,a=e.seq.charAt(i);a&&(n.ref=a);var s=o[a];void 0===s&&(s=4);var f=r.substitutionMatrix[s][n.data];f&&(n.sub=f)}}(0,t,e,r)})),!this.readBases&&t.start<=this.alignmentStart&&t.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=t)},t.prototype.toJSON=function(){var t=this,e={};return Object.keys(this).forEach((function(r){"_"!==r.charAt(0)&&(e[r]=t[r])})),e.readBases=this.getReadBases(),e},t}();e.default=a},function(t,e,r){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var n=r(0),i=r(68),o={BF:"int",CF:"int",RI:"int",RL:"int",AP:"int",RG:"int",MF:"int",NS:"int",NP:"int",TS:"int",NF:"int",TC:"byte",TN:"int",FN:"int",FC:"byte",FP:"int",BS:"byte",IN:"byteArray",SC:"byteArray",DL:"int",BA:"byte",BB:"byteArray",RS:"int",PD:"int",HC:"int",MQ:"int",RN:"byteArray",QS:"byte",QQ:"byteArray",TL:"int",TM:"ignore",TV:"ignore"};var a=function(){function t(t){Object.assign(this,t),this.readNamesIncluded=t.preservation.RN,this.APdelta=t.preservation.AP,this.referenceRequired=!!t.preservation.RR,this.tagIdsDictionary=t.preservation.TD,this.substitutionMatrix=function(t){for(var e=new Array(5),r=0;r<5;r+=1)e[r]=new Array(4);return e[0][t[0]>>6&3]="C",e[0][t[0]>>4&3]="G",e[0][t[0]>>2&3]="T",e[0][t[0]>>0&3]="N",e[1][t[1]>>6&3]="A",e[1][t[1]>>4&3]="G",e[1][t[1]>>2&3]="T",e[1][t[1]>>0&3]="N",e[2][t[2]>>6&3]="A",e[2][t[2]>>4&3]="C",e[2][t[2]>>2&3]="T",e[2][t[2]>>0&3]="N",e[3][t[3]>>6&3]="A",e[3][t[3]>>4&3]="C",e[3][t[3]>>2&3]="G",e[3][t[3]>>0&3]="N",e[4][t[4]>>6&3]="A",e[4][t[4]>>4&3]="C",e[4][t[4]>>2&3]="G",e[4][t[4]>>0&3]="T",e}(t.preservation.SM),this.dataSeriesCodecCache=new Map,this.tagCodecCache={}}return t.prototype.getCodecForTag=function(t){if(!this.tagCodecCache[t]){var e=this.tagEncoding[t];e&&(this.tagCodecCache[t]=(0,i.instantiateCodec)(e,"byteArray"))}return this.tagCodecCache[t]},t.prototype.getTagNames=function(t){return this.tagIdsDictionary[t]},t.prototype.getCodecForDataSeries=function(t){var e=this.dataSeriesCodecCache.get(t);if(void 0===e){var r=this.dataSeriesEncoding[t];if(r){var a=o[t];if(!a)throw new n.CramMalformedError("data series name ".concat(t," not defined in file compression header"));e=(0,i.instantiateCodec)(r,a),this.dataSeriesCodecCache.set(t,e)}}return e},t.prototype.toJSON=function(){var t=this,e={};return Object.keys(this).forEach((function(r){/Cache$/.test(r)||(e[r]=t[r])})),e},t}();e.default=a},function(t,e,r){"use strict";var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0}),e.instantiateCodec=e.getCodecClassWithId=void 0;var i=r(0),o=n(r(69)),a=n(r(70)),s=n(r(71)),f=n(r(72)),u=n(r(73)),c=n(r(74)),h=n(r(75)),l={1:a.default,3:o.default,4:f.default,5:s.default,6:u.default,7:h.default,9:c.default};function d(t){return l[t]}e.getCodecClassWithId=d,e.instantiateCodec=function t(e,r){var n=d("ignore"===r?0:e.codecId);if(!n)throw new i.CramUnimplementedError("no codec implemented for codec ID ".concat(e.codecId));return new n(e.parameters,r,t)}},function(t,e,r){"use strict";var n,i=this&&this.__extends||(n=function(t,e){return(n=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&(t[r]=e[r])})(t,e)},function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");function r(){this.constructor=t}n(t,e),t.prototype=null===e?Object.create(e):(r.prototype=e.prototype,new r)}),o=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var a=r(0);var s=function(t){function e(e,r){void 0===e&&(e={});var n=t.call(this,e,r)||this;if(!["byte","int"].includes(n.dataType))throw new TypeError("".concat(n.dataType," decoding not yet implemented by HUFFMAN_INT codec"));return n.buildCodeBook(),n.buildCodes(),n.buildCaches(),0===n.sortedCodes[0].bitLength&&(n._decode=n._decodeZeroLengthCode),n}return i(e,t),e.prototype.buildCodeBook=function(){for(var t=this,e=new Array(this.parameters.numCodes),r=0;r<this.parameters.numCodes;r+=1)e[r]={symbol:this.parameters.symbols[r],bitLength:this.parameters.bitLengths[r]};e=e.sort((function(t,e){return t.bitLength-e.bitLength||t.symbol-e.symbol})),this.codeBook={},e.forEach((function(e){t.codeBook[e.bitLength]||(t.codeBook[e.bitLength]=[]),t.codeBook[e.bitLength].push(e.symbol)}))},e.prototype.buildCodes=function(){var t=this;this.codes={};var e=0,r=-1;Object.entries(this.codeBook).forEach((function(n){var i=n[0],o=n[1];i=parseInt(i,10),o.forEach((function(n){var o={bitLength:i,value:n};r+=1;var s,f,u=i-e;if(r<<=u,o.bitCode=r,e+=u,16843009*((f=(858993459&(f=(s=r)-(s>>1)&1431655765))+(f>>2&858993459))+(f>>4)&252645135)>>24>i)throw new a.CramMalformedError("Symbol out of range");t.codes[n]=o}))}))},e.prototype.buildCaches=function(){this.sortedCodes=Object.values(this.codes).sort((function(t,e){return t.bitLength-e.bitLength||t.bitCode-e.bitCode})),this.sortedByValue=Object.values(this.codes).sort((function(t,e){return t.value-e.value})),this.sortedValuesByBitCode=this.sortedCodes.map((function(t){return t.value})),this.sortedBitCodes=this.sortedCodes.map((function(t){return t.bitCode})),this.sortedBitLengthsByBitCode=this.sortedCodes.map((function(t){return t.bitLength}));var t=Math.max.apply(Math,this.sortedBitCodes);this.bitCodeToValue=new Array(t+1).fill(-1);for(var e=0;e<this.sortedBitCodes.length;e+=1)this.bitCodeToValue[this.sortedCodes[e].bitCode]=e},e.prototype.decode=function(t,e,r,n){return this._decode(t,e,n.coreBlock)},e.prototype._decodeZeroLengthCode=function(){return this.sortedCodes[0].value},e.prototype._decode=function(t,e,r){for(var n=e.content,i=0,o=0,s=0;s<this.sortedCodes.length;s+=1){var f=this.sortedCodes[s].bitLength;o<<=f-i,o|=this._getBits(n,r,f-i),i=f;var u=this.bitCodeToValue[o];if(u>-1&&this.sortedBitLengthsByBitCode[u]===f)return this.sortedValuesByBitCode[u];for(var c=s;this.sortedCodes[c+1].bitLength===f&&c<this.sortedCodes.length;c+=1)s+=1}throw new a.CramMalformedError("Huffman symbol not found.")},e}(o(r(3)).default);e.default=s},function(t,e,r){"use strict";var n,i=this&&this.__extends||(n=function(t,e){return(n=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&(t[r]=e[r])})(t,e)},function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");function r(){this.constructor=t}n(t,e),t.prototype=null===e?Object.create(e):(r.prototype=e.prototype,new r)}),o=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var a=r(0),s=o(r(3)),f=r(5),u=function(t){function e(e,r){void 0===e&&(e={});var n=t.call(this,e,r)||this;if("int"===n.dataType)n._decodeData=n._decodeInt;else{if("byte"!==n.dataType)throw new a.CramUnimplementedError("".concat(n.dataType," decoding not yet implemented by EXTERNAL codec"));n._decodeData=n._decodeByte}return n}return i(e,t),e.prototype.decode=function(t,e,r,n){var i=this.parameters.blockContentId,o=r[i];if(!o)throw new a.CramMalformedError("no block found with content ID ".concat(i));var s=n.externalBlocks.getCursor(i);return this._decodeData(o,s)},e.prototype._decodeInt=function(t,e){var r=(0,f.parseItf8)(t.content,e.bytePosition),n=r[0],i=r[1];return e.bytePosition+=i,n},e.prototype._decodeByte=function(t,e){if(e.bytePosition>=t.content.length)throw new a.CramBufferOverrunError("attempted to read beyond end of block. this file seems truncated.");return t.content[e.bytePosition++]},e}(s.default);e.default=u},function(t,e,r){"use strict";var n,i=this&&this.__extends||(n=function(t,e){return(n=Object.setPrototypeOf||{__proto__:[]}instanceof 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package/esm/craiIndex.js

@@ -138,7 +138,7 @@ export default class CraiIndex {
         const compare = entry => {
             const entryStart = entry.start;
             const entryEnd = entry.start + entry.span;
-            if (entryStart >= queryEnd) {
+            if (entryStart > queryEnd) {
                 return -1;
             } // entry is ahead of query
             if (entryEnd <= queryStart) {

package/esm/craiIndex.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "1.6.3",
+  "version": "1.6.4",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",

package/src/craiIndex.js

@@ -161,7 +161,7 @@ export default class CraiIndex {
     const compare = entry => {
       const entryStart = entry.start
       const entryEnd = entry.start + entry.span
-      if (entryStart >= queryEnd) {
+      if (entryStart > queryEnd) {
         return -1
       } // entry is ahead of query
       if (entryEnd <= queryStart) {