@gmod/cram 1.6.3 → 1.7.0

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/filehandle.d.ts

@@ -0,0 +1,2 @@
+import { GenericFilehandle } from 'generic-filehandle';
+export { GenericFilehandle as Filehandle };

package/dist/cramFile/filehandle.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=filehandle.js.map

package/dist/cramFile/filehandle.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"filehandle.js","sourceRoot":"","sources":["../../src/cramFile/filehandle.ts"],"names":[],"mappings":""}

package/dist/cramFile/index.d.ts

@@ -1,2 +1,2 @@
+import CramFile from './file';
 export default CramFile;
-import CramFile from "./file";

package/dist/cramFile/index.js

@@ -3,6 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var file_1 = __importDefault(require("./file"));
+const file_1 = __importDefault(require("./file"));
 exports.default = file_1.default;
 //# sourceMappingURL=index.js.map

package/dist/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.js"],"names":[],"mappings":";;;;;AAAA,gDAA6B;AAE7B,kBAAe,cAAQ,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;AAAA,kDAA6B;AAE7B,kBAAe,cAAQ,CAAA"}

package/dist/cramFile/record.d.ts

@@ -1,8 +1,63 @@
+import CramContainerCompressionScheme from './container/compressionScheme';
+import decodeRecord from './slice/decodeRecord';
+export declare type RefRegion = {
+    start: number;
+    end: number;
+    seq: string;
+};
+export declare type ReadFeature = {
+    code: string;
+    pos: number;
+    refPos: number;
+    data: any;
+    ref?: string;
+    sub?: string;
+};
+export declare type MateRecord = {
+    readName?: string;
+    sequenceId: number;
+    alignmentStart: number;
+    flags?: number;
+    uniqueId?: number;
+};
+export declare const BamFlags: readonly [readonly [1, "Paired"], readonly [2, "ProperlyPaired"], readonly [4, "SegmentUnmapped"], readonly [8, "MateUnmapped"], readonly [16, "ReverseComplemented"], readonly [32, "MateReverseComplemented"], readonly [64, "Read1"], readonly [128, "Read2"], readonly [256, "Secondary"], readonly [512, "FailedQc"], readonly [1024, "Duplicate"], readonly [2048, "Supplementary"]];
+export declare const CramFlags: readonly [readonly [1, "PreservingQualityScores"], readonly [2, "Detached"], readonly [4, "WithMateDownstream"], readonly [8, "DecodeSequenceAsStar"]];
+export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];
+declare type FlagsDecoder<Type> = {
+    [Property in Type as `is${Capitalize<string & Property>}`]: (flags: number) => boolean;
+};
+declare type FlagsEncoder<Type> = {
+    [Property in Type as `set${Capitalize<string & Property>}`]: (flags: number) => number;
+};
+export declare const BamFlagsDecoder: FlagsDecoder<"Paired" | "ProperlyPaired" | "SegmentUnmapped" | "MateUnmapped" | "ReverseComplemented" | "MateReverseComplemented" | "Read1" | "Read2" | "Secondary" | "FailedQc" | "Duplicate" | "Supplementary"> & FlagsEncoder<"Paired" | "ProperlyPaired" | "SegmentUnmapped" | "MateUnmapped" | "ReverseComplemented" | "MateReverseComplemented" | "Read1" | "Read2" | "Secondary" | "FailedQc" | "Duplicate" | "Supplementary">;
+export declare const CramFlagsDecoder: FlagsDecoder<"PreservingQualityScores" | "Detached" | "WithMateDownstream" | "DecodeSequenceAsStar"> & FlagsEncoder<"PreservingQualityScores" | "Detached" | "WithMateDownstream" | "DecodeSequenceAsStar">;
+export declare const MateFlagsDecoder: FlagsDecoder<"OnNegativeStrand" | "Unmapped"> & FlagsEncoder<"OnNegativeStrand" | "Unmapped">;
 /**
  * Class of each CRAM record returned by this API.
  */
 export default class CramRecord {
-    tags: {};
+    tags: Record<string, string>;
+    flags: number;
+    cramFlags: number;
+    readBases?: string | null;
+    _refRegion?: RefRegion;
+    readFeatures?: ReadFeature[];
+    alignmentStart: number;
+    lengthOnRef: number | undefined;
+    readLength: number;
+    templateLength?: number;
+    templateSize?: number;
+    readName?: string;
+    mateRecordNumber?: number;
+    mate?: MateRecord;
+    uniqueId: number;
+    sequenceId: number;
+    readGroupId: number;
+    mappingQuality: number | undefined;
+    qualityScores: number[] | null | undefined;
+    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }: ReturnType<typeof decodeRecord> & {
+        uniqueId: number;
+    });
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */
@@ -43,13 +98,12 @@ export default class CramRecord {
      * Get the original sequence of this read.
      * @returns {String} sequence basepairs
      */
-    getReadBases(): string;
-    readBases: any;
+    getReadBases(): string | null | undefined;
     /**
      * Get the pair orientation of a paired read. Adapted from igv.js
      * @returns {String} of paired orientatin
      */
-    getPairOrientation(): string;
+    getPairOrientation(): string | null;
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
@@ -63,17 +117,7 @@ export default class CramRecord {
      * @param {CramContainerCompressionScheme} compressionScheme
      * @returns {undefined} nothing
      */
-    addReferenceSequence(refRegion: {
-        start: number;
-        end: number;
-        seq: string;
-    }, compressionScheme: CramContainerCompressionScheme): undefined;
-    _refRegion: {
-        start: number;
-        end: number;
-        seq: string;
-    } | undefined;
-    toJSON(): {
-        readBases: string;
-    };
+    addReferenceSequence(refRegion: RefRegion, compressionScheme: CramContainerCompressionScheme): void;
+    toJSON(): any;
 }
+export {};

package/dist/cramFile/record.js

@@ -3,28 +3,29 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var constants_1 = __importDefault(require("./constants"));
+exports.MateFlagsDecoder = exports.CramFlagsDecoder = exports.BamFlagsDecoder = exports.MateFlags = exports.CramFlags = exports.BamFlags = void 0;
+const constants_1 = __importDefault(require("./constants"));
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
-        return undefined;
+        return null;
     }
     if (cramRecord.isUnknownBases()) {
-        return undefined;
+        return null;
     }
     // remember: all coordinates are 1-based closed
-    var regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
+    const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
     if (!cramRecord.readFeatures) {
         return refRegion.seq
             .substr(regionSeqOffset, cramRecord.lengthOnRef)
             .toUpperCase();
     }
-    var bases = '';
-    var regionPos = regionSeqOffset;
-    var currentReadFeature = 0;
+    let bases = '';
+    let regionPos = regionSeqOffset;
+    let currentReadFeature = 0;
     while (bases.length < cramRecord.readLength) {
         if (currentReadFeature < cramRecord.readFeatures.length) {
-            var feature = cramRecord.readFeatures[currentReadFeature];
+            const feature = cramRecord.readFeatures[currentReadFeature];
             if (feature.code === 'Q' || feature.code === 'q') {
                 currentReadFeature += 1;
             }
@@ -33,8 +34,8 @@ function decodeReadSequence(cramRecord, refRegion) {
                 currentReadFeature += 1;
                 if (feature.code === 'b') {
                     // specify a base pair for some reason
-                    var ret = feature.data.split(',');
-                    var added = String.fromCharCode.apply(String, ret);
+                    const ret = feature.data.split(',');
+                    const added = String.fromCharCode(...ret);
                     bases += added;
                     regionPos += added.length;
                 }
@@ -81,21 +82,21 @@ function decodeReadSequence(cramRecord, refRegion) {
             }
             else if (currentReadFeature < cramRecord.readFeatures.length) {
                 // put down a chunk of sequence up to the next read feature
-                var chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                const chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
                 bases += chunk;
                 regionPos += chunk.length;
             }
         }
         else {
             // put down a chunk of reference up to the full read length
-            var chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            const chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
             bases += chunk;
             regionPos += chunk.length;
         }
     }
     return bases.toUpperCase();
 }
-var baseNumbers = {
+const baseNumbers = {
     a: 0,
     A: 0,
     c: 1,
@@ -112,120 +113,195 @@ function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFe
         return;
     }
     // decode base substitution code using the substitution matrix
-    var refCoord = readFeature.refPos - refRegion.start;
-    var refBase = refRegion.seq.charAt(refCoord);
+    const refCoord = readFeature.refPos - refRegion.start;
+    const refBase = refRegion.seq.charAt(refCoord);
     if (refBase) {
         readFeature.ref = refBase;
     }
-    var baseNumber = baseNumbers[refBase];
+    let baseNumber = baseNumbers[refBase];
     if (baseNumber === undefined) {
         baseNumber = 4;
     }
-    var substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
-    var base = substitutionScheme[readFeature.data];
+    const substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
+    const base = substitutionScheme[readFeature.data];
     if (base) {
         readFeature.sub = base;
     }
 }
+exports.BamFlags = [
+    [0x1, 'Paired'],
+    [0x2, 'ProperlyPaired'],
+    [0x4, 'SegmentUnmapped'],
+    [0x8, 'MateUnmapped'],
+    [0x10, 'ReverseComplemented'],
+    //  the mate is mapped to the reverse strand
+    [0x20, 'MateReverseComplemented'],
+    //  this is read1
+    [0x40, 'Read1'],
+    //  this is read2
+    [0x80, 'Read2'],
+    //  not primary alignment
+    [0x100, 'Secondary'],
+    //  QC failure
+    [0x200, 'FailedQc'],
+    //  optical or PCR duplicate
+    [0x400, 'Duplicate'],
+    //  supplementary alignment
+    [0x800, 'Supplementary'],
+];
+exports.CramFlags = [
+    [0x1, 'PreservingQualityScores'],
+    [0x2, 'Detached'],
+    [0x4, 'WithMateDownstream'],
+    [0x8, 'DecodeSequenceAsStar'],
+];
+exports.MateFlags = [
+    [0x1, 'OnNegativeStrand'],
+    [0x2, 'Unmapped'],
+];
+function makeFlagsHelper(x) {
+    const r = {};
+    for (const [code, name] of x) {
+        r['is' + name] = (flags) => !!(flags & code);
+        r['set' + name] = (flags) => flags | code;
+    }
+    return r;
+}
+exports.BamFlagsDecoder = makeFlagsHelper(exports.BamFlags);
+exports.CramFlagsDecoder = makeFlagsHelper(exports.CramFlags);
+exports.MateFlagsDecoder = makeFlagsHelper(exports.MateFlags);
 /**
  * Class of each CRAM record returned by this API.
  */
-var CramRecord = /** @class */ (function () {
-    function CramRecord() {
-        this.tags = {};
+class CramRecord {
+    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }) {
+        this.flags = flags;
+        this.cramFlags = cramFlags;
+        this.readLength = readLength;
+        this.mappingQuality = mappingQuality;
+        this.lengthOnRef = lengthOnRef;
+        this.qualityScores = qualityScores;
+        if (readBases) {
+            this.readBases = readBases;
+        }
+        this.readGroupId = readGroupId;
+        this.readName = readName;
+        this.sequenceId = sequenceId;
+        this.uniqueId = uniqueId;
+        this.templateSize = templateSize;
+        this.alignmentStart = alignmentStart;
+        this.tags = tags;
+        // backwards compatibility
+        if (readFeatures) {
+            this.readFeatures = readFeatures;
+        }
+        if (mateToUse) {
+            this.mate = {
+                flags: mateToUse.mateFlags,
+                readName: mateToUse.mateReadName,
+                sequenceId: mateToUse.mateSequenceId,
+                alignmentStart: mateToUse.mateAlignmentStart,
+            };
+        }
+        if (mateRecordNumber) {
+            this.mateRecordNumber = mateRecordNumber;
+        }
     }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */
-    CramRecord.prototype.isPaired = function () {
+    isPaired() {
         return !!(this.flags & constants_1.default.BAM_FPAIRED);
-    };
+    }
     /** @returns {boolean} true if the read is paired, and both segments are mapped */
-    CramRecord.prototype.isProperlyPaired = function () {
+    isProperlyPaired() {
         return !!(this.flags & constants_1.default.BAM_FPROPER_PAIR);
-    };
+    }
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-    CramRecord.prototype.isSegmentUnmapped = function () {
+    isSegmentUnmapped() {
         return !!(this.flags & constants_1.default.BAM_FUNMAP);
-    };
+    }
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-    CramRecord.prototype.isMateUnmapped = function () {
+    isMateUnmapped() {
         return !!(this.flags & constants_1.default.BAM_FMUNMAP);
-    };
+    }
     /** @returns {boolean} true if the read is mapped to the reverse strand */
-    CramRecord.prototype.isReverseComplemented = function () {
+    isReverseComplemented() {
         return !!(this.flags & constants_1.default.BAM_FREVERSE);
-    };
+    }
     /** @returns {boolean} true if the mate is mapped to the reverse strand */
-    CramRecord.prototype.isMateReverseComplemented = function () {
+    isMateReverseComplemented() {
         return !!(this.flags & constants_1.default.BAM_FMREVERSE);
-    };
+    }
     /** @returns {boolean} true if this is read number 1 in a pair */
-    CramRecord.prototype.isRead1 = function () {
+    isRead1() {
         return !!(this.flags & constants_1.default.BAM_FREAD1);
-    };
+    }
     /** @returns {boolean} true if this is read number 2 in a pair */
-    CramRecord.prototype.isRead2 = function () {
+    isRead2() {
         return !!(this.flags & constants_1.default.BAM_FREAD2);
-    };
+    }
     /** @returns {boolean} true if this is a secondary alignment */
-    CramRecord.prototype.isSecondary = function () {
+    isSecondary() {
         return !!(this.flags & constants_1.default.BAM_FSECONDARY);
-    };
+    }
     /** @returns {boolean} true if this read has failed QC checks */
-    CramRecord.prototype.isFailedQc = function () {
+    isFailedQc() {
         return !!(this.flags & constants_1.default.BAM_FQCFAIL);
-    };
+    }
     /** @returns {boolean} true if the read is an optical or PCR duplicate */
-    CramRecord.prototype.isDuplicate = function () {
+    isDuplicate() {
         return !!(this.flags & constants_1.default.BAM_FDUP);
-    };
+    }
     /** @returns {boolean} true if this is a supplementary alignment */
-    CramRecord.prototype.isSupplementary = function () {
+    isSupplementary() {
         return !!(this.flags & constants_1.default.BAM_FSUPPLEMENTARY);
-    };
+    }
     /**
      * @returns {boolean} true if the read is detached
      */
-    CramRecord.prototype.isDetached = function () {
+    isDetached() {
         return !!(this.cramFlags & constants_1.default.CRAM_FLAG_DETACHED);
-    };
+    }
     /** @returns {boolean} true if the read has a mate in this same CRAM segment */
-    CramRecord.prototype.hasMateDownStream = function () {
+    hasMateDownStream() {
         return !!(this.cramFlags & constants_1.default.CRAM_FLAG_MATE_DOWNSTREAM);
-    };
+    }
     /** @returns {boolean} true if the read contains qual scores */
-    CramRecord.prototype.isPreservingQualityScores = function () {
+    isPreservingQualityScores() {
         return !!(this.cramFlags & constants_1.default.CRAM_FLAG_PRESERVE_QUAL_SCORES);
-    };
+    }
     /** @returns {boolean} true if the read has no sequence bases */
-    CramRecord.prototype.isUnknownBases = function () {
+    isUnknownBases() {
         return !!(this.cramFlags & constants_1.default.CRAM_FLAG_NO_SEQ);
-    };
+    }
     /**
      * Get the original sequence of this read.
      * @returns {String} sequence basepairs
      */
-    CramRecord.prototype.getReadBases = function () {
+    getReadBases() {
         if (!this.readBases && this._refRegion) {
-            this.readBases = decodeReadSequence(this, this._refRegion);
+            const decoded = decodeReadSequence(this, this._refRegion);
+            if (decoded) {
+                this.readBases = decoded;
+            }
         }
         return this.readBases;
-    };
+    }
     /**
      * Get the pair orientation of a paired read. Adapted from igv.js
      * @returns {String} of paired orientatin
      */
-    CramRecord.prototype.getPairOrientation = function () {
+    getPairOrientation() {
         if (!this.isSegmentUnmapped() &&
             this.isPaired() &&
             !this.isMateUnmapped() &&
             this.mate &&
             this.sequenceId === this.mate.sequenceId) {
-            var s1 = this.isReverseComplemented() ? 'R' : 'F';
-            var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            var o1 = ' ';
-            var o2 = ' ';
+            const s1 = this.isReverseComplemented() ? 'R' : 'F';
+            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
+            let o1 = ' ';
+            let o2 = ' ';
             if (this.isRead1()) {
                 o1 = '1';
                 o2 = '2';
@@ -234,8 +310,11 @@ var CramRecord = /** @class */ (function () {
                 o1 = '2';
                 o2 = '1';
             }
-            var tmp = [];
-            var isize = this.templateLength || this.templateSize;
+            const tmp = [];
+            let isize = this.templateLength || this.templateSize;
+            if (isize === undefined) {
+                throw new Error('One of templateSize and templateLength must be set');
+            }
             if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
                 isize = -isize;
             }
@@ -254,7 +333,7 @@ var CramRecord = /** @class */ (function () {
             return tmp.join('');
         }
         return null;
-    };
+    }
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
@@ -268,14 +347,13 @@ var CramRecord = /** @class */ (function () {
      * @param {CramContainerCompressionScheme} compressionScheme
      * @returns {undefined} nothing
      */
-    CramRecord.prototype.addReferenceSequence = function (refRegion, compressionScheme) {
-        var _this = this;
+    addReferenceSequence(refRegion, compressionScheme) {
         if (this.readFeatures) {
             // use the reference bases to decode the bases
             // substituted in each base substitution
-            this.readFeatures.forEach(function (readFeature) {
+            this.readFeatures.forEach(readFeature => {
                 if (readFeature.code === 'X') {
-                    decodeBaseSubstitution(_this, refRegion, compressionScheme, readFeature);
+                    decodeBaseSubstitution(this, refRegion, compressionScheme, readFeature);
                 }
             });
         }
@@ -287,20 +365,18 @@ var CramRecord = /** @class */ (function () {
                 this.alignmentStart + (this.lengthOnRef || this.readLength) - 1) {
             this._refRegion = refRegion;
         }
-    };
-    CramRecord.prototype.toJSON = function () {
-        var _this = this;
-        var data = {};
-        Object.keys(this).forEach(function (k) {
+    }
+    toJSON() {
+        const data = {};
+        Object.keys(this).forEach(k => {
             if (k.charAt(0) === '_') {
                 return;
             }
-            data[k] = _this[k];
+            data[k] = this[k];
         });
         data.readBases = this.getReadBases();
         return data;
-    };
-    return CramRecord;
-}());
+    }
+}
 exports.default = CramRecord;
 //# sourceMappingURL=record.js.map

package/dist/cramFile/record.js.map

@@ -1 +1 @@
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