@gmod/cram 1.6.3 → 1.7.0

package/dist/cramFile/slice/decodeRecord.js

@@ -3,17 +3,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var long_1 = __importDefault(require("long"));
-var errors_1 = require("../../errors");
-var record_1 = __importDefault(require("../record"));
-var constants_1 = __importDefault(require("../constants"));
+const long_1 = __importDefault(require("long"));
+const errors_1 = require("../../errors");
+const record_1 = require("../record");
+const sectionParsers_1 = require("../sectionParsers");
 /**
  * given a Buffer, read a string up to the first null character
  * @private
  */
 function readNullTerminatedString(buffer) {
-    var r = '';
-    for (var i = 0; i < buffer.length && buffer[i] !== 0; i++) {
+    let r = '';
+    for (let i = 0; i < buffer.length && buffer[i] !== 0; i++) {
         r += String.fromCharCode(buffer[i]);
     }
     return r;
@@ -23,49 +23,49 @@ function readNullTerminatedString(buffer) {
  * @private
  */
 function parseTagValueArray(buffer) {
-    var arrayType = String.fromCharCode(buffer[0]);
-    var length = Int32Array.from(buffer.slice(1))[0];
-    var array = new Array(length);
+    const arrayType = String.fromCharCode(buffer[0]);
+    const length = Int32Array.from(buffer.slice(1))[0];
+    const array = new Array(length);
     buffer = buffer.slice(5);
     if (arrayType === 'c') {
-        var arr = new Int8Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Int8Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'C') {
-        var arr = new Uint8Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Uint8Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 's') {
-        var arr = new Int16Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Int16Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'S') {
-        var arr = new Uint16Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Uint16Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'i') {
-        var arr = new Int32Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Int32Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'I') {
-        var arr = new Uint32Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Uint32Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'f') {
-        var arr = new Float32Array(buffer.buffer);
-        for (var i = 0; i < length; i += 1) {
+        const arr = new Float32Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
             array[i] = arr[i];
         }
     }
@@ -108,15 +108,14 @@ function parseTagData(tagType, buffer) {
     if (tagType === 'B') {
         return parseTagValueArray(buffer);
     }
-    throw new errors_1.CramMalformedError("Unrecognized tag type ".concat(tagType));
+    throw new errors_1.CramMalformedError(`Unrecognized tag type ${tagType}`);
 }
-function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
-    var currentReadPos = 0;
-    var currentRefPos = cramRecord.alignmentStart - 1;
-    var readFeatures = new Array(readFeatureCount);
-    function decodeRFData(_a) {
-        var type = _a[0], dataSeriesName = _a[1];
-        var data = decodeDataSeries(dataSeriesName);
+function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
+    let currentReadPos = 0;
+    let currentRefPos = alignmentStart - 1;
+    const readFeatures = new Array(readFeatureCount);
+    function decodeRFData([type, dataSeriesName]) {
+        const data = decodeDataSeries(dataSeriesName);
         if (type === 'character') {
             return String.fromCharCode(data);
         }
@@ -131,12 +130,11 @@ function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, comp
         // }
         return data;
     }
-    for (var i = 0; i < readFeatureCount; i += 1) {
-        var code = String.fromCharCode(decodeDataSeries('FC'));
-        var readPosDelta = decodeDataSeries('FP');
-        var readFeature = { code: code };
+    for (let i = 0; i < readFeatureCount; i += 1) {
+        const code = String.fromCharCode(decodeDataSeries('FC'));
+        const readPosDelta = decodeDataSeries('FP');
         // map of operator name -> data series name
-        var data1Schema = {
+        const data1Schema = {
             B: ['character', 'BA'],
             S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
             X: ['number', 'BS'],
@@ -151,161 +149,193 @@ function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, comp
             N: ['number', 'RS'],
         }[code];
         if (!data1Schema) {
-            throw new errors_1.CramMalformedError("invalid read feature code \"".concat(code, "\""));
+            throw new errors_1.CramMalformedError(`invalid read feature code "${code}"`);
         }
-        readFeature.data = decodeRFData(data1Schema);
+        let data = decodeRFData(data1Schema);
         // if this is a tag with two data items, make the data an array and add the second item
-        var data2Schema = { B: ['number', 'QS'] }[code];
+        const data2Schema = { B: ['number', 'QS'] }[code];
         if (data2Schema) {
-            readFeature.data = [readFeature.data, decodeRFData(data2Schema)];
+            data = [data, decodeRFData(data2Schema)];
         }
         currentReadPos += readPosDelta;
-        readFeature.pos = currentReadPos;
+        const pos = currentReadPos;
         currentRefPos += readPosDelta;
-        readFeature.refPos = currentRefPos;
+        const refPos = currentRefPos;
         // for gapping features, adjust the reference position for read features that follow
         if (code === 'D' || code === 'N') {
-            currentRefPos += readFeature.data;
+            currentRefPos += data;
         }
         else if (code === 'I' || code === 'S') {
-            currentRefPos -= readFeature.data.length;
+            currentRefPos -= data.length;
         }
         else if (code === 'i') {
             currentRefPos -= 1;
         }
-        readFeatures[i] = readFeature;
+        readFeatures[i] = { code, pos, refPos, data };
     }
     return readFeatures;
 }
 function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
-    var cramRecord = new record_1.default();
-    cramRecord.flags = decodeDataSeries('BF');
+    let flags = decodeDataSeries('BF');
     // note: the C data type of compressionFlags is byte in cram v1
     // and int32 in cram v2+, but that does not matter for us here
     // in javascript land.
-    cramRecord.cramFlags = decodeDataSeries('CF');
-    if (majorVersion > 1 && sliceHeader.content.refSeqId === -2) {
-        cramRecord.sequenceId = decodeDataSeries('RI');
+    const cramFlags = decodeDataSeries('CF');
+    if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent)) {
+        throw new Error();
+    }
+    let sequenceId;
+    if (majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2) {
+        sequenceId = decodeDataSeries('RI');
     }
     else {
-        cramRecord.sequenceId = sliceHeader.content.refSeqId;
+        sequenceId = sliceHeader.parsedContent.refSeqId;
     }
-    cramRecord.readLength = decodeDataSeries('RL');
+    const readLength = decodeDataSeries('RL');
     // if APDelta, will calculate the true start in a second pass
-    cramRecord.alignmentStart = decodeDataSeries('AP');
+    let alignmentStart = decodeDataSeries('AP');
     if (compressionScheme.APdelta) {
-        cramRecord.alignmentStart += cursors.lastAlignmentStart;
+        alignmentStart = alignmentStart + cursors.lastAlignmentStart;
     }
-    cursors.lastAlignmentStart = cramRecord.alignmentStart;
-    cramRecord.readGroupId = decodeDataSeries('RG');
+    cursors.lastAlignmentStart = alignmentStart;
+    const readGroupId = decodeDataSeries('RG');
+    let readName;
     if (compressionScheme.readNamesIncluded) {
-        cramRecord.readName = readNullTerminatedString(decodeDataSeries('RN'));
+        readName = readNullTerminatedString(decodeDataSeries('RN'));
     }
+    let mateToUse;
+    let templateSize;
+    let mateRecordNumber;
     // mate record
-    if (cramRecord.isDetached()) {
+    if (record_1.CramFlagsDecoder.isDetached(cramFlags)) {
         // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-        var mate = {};
-        mate.flags = decodeDataSeries('MF');
+        // const mate: any = {}
+        const mateFlags = decodeDataSeries('MF');
+        let mateReadName;
         if (!compressionScheme.readNamesIncluded) {
-            mate.readName = readNullTerminatedString(decodeDataSeries('RN'));
-            cramRecord.readName = mate.readName;
+            mateReadName = readNullTerminatedString(decodeDataSeries('RN'));
+            readName = mateReadName;
         }
-        mate.sequenceId = decodeDataSeries('NS');
-        mate.alignmentStart = decodeDataSeries('NP');
-        if (mate.flags || mate.sequenceId > -1) {
-            cramRecord.mate = mate;
+        const mateSequenceId = decodeDataSeries('NS');
+        const mateAlignmentStart = decodeDataSeries('NP');
+        if (mateFlags || mateSequenceId > -1) {
+            mateToUse = {
+                mateFlags,
+                mateSequenceId,
+                mateAlignmentStart,
+                mateReadName,
+            };
         }
-        cramRecord.templateSize = decodeDataSeries('TS');
+        templateSize = decodeDataSeries('TS');
         // set mate unmapped if needed
-        if (mate.flags & constants_1.default.CRAM_M_UNMAP) {
-            cramRecord.flags |= constants_1.default.BAM_FMUNMAP;
+        if (record_1.MateFlagsDecoder.isUnmapped(mateFlags)) {
+            flags = record_1.BamFlagsDecoder.setMateUnmapped(flags);
         }
         // set mate reversed if needed
-        if (mate.flags & constants_1.default.CRAM_M_REVERSE) {
-            cramRecord.flags |= constants_1.default.BAM_FMREVERSE;
+        if (record_1.MateFlagsDecoder.isOnNegativeStrand(mateFlags)) {
+            flags = record_1.BamFlagsDecoder.setMateReverseComplemented(flags);
         }
         // detachedCount++
     }
-    else if (cramRecord.hasMateDownStream()) {
-        cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
+    else if (record_1.CramFlagsDecoder.isWithMateDownstream(cramFlags)) {
+        mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
     }
     // TODO: the aux tag parsing will have to be refactored if we want to support
     // cram v1
-    var TLindex = decodeDataSeries('TL');
+    const TLindex = decodeDataSeries('TL');
     if (TLindex < 0) {
         /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
         throw new errors_1.CramMalformedError('invalid TL index');
     }
+    const tags = {};
     // TN = tag names
-    var TN = compressionScheme.getTagNames(TLindex);
-    var ntags = TN.length;
-    for (var i = 0; i < ntags; i += 1) {
-        var tagId = TN[i];
-        var tagName = tagId.substr(0, 2);
-        var tagType = tagId.substr(2, 1);
-        var tagCodec = compressionScheme.getCodecForTag(tagId);
+    const TN = compressionScheme.getTagNames(TLindex);
+    const ntags = TN.length;
+    for (let i = 0; i < ntags; i += 1) {
+        const tagId = TN[i];
+        const tagName = tagId.substr(0, 2);
+        const tagType = tagId.substr(2, 1);
+        const tagCodec = compressionScheme.getCodecForTag(tagId);
         if (!tagCodec) {
-            throw new errors_1.CramMalformedError("no codec defined for auxiliary tag ".concat(tagId));
+            throw new errors_1.CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);
         }
-        var tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-        cramRecord.tags[tagName] = parseTagData(tagType, tagData);
-    }
-    if (!cramRecord.isSegmentUnmapped()) {
+        const tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        tags[tagName] = parseTagData(tagType, tagData);
+    }
+    let readFeatures;
+    let lengthOnRef;
+    let mappingQuality;
+    let qualityScores;
+    let readBases = undefined;
+    if (!record_1.BamFlagsDecoder.isSegmentUnmapped(flags)) {
         // reading read features
-        var /* int */ readFeatureCount = decodeDataSeries('FN');
+        const readFeatureCount = decodeDataSeries('FN');
         if (readFeatureCount) {
-            cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
+            readFeatures = decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
         }
         // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
-        var lengthOnRef_1 = cramRecord.readLength;
-        if (cramRecord.readFeatures) {
-            cramRecord.readFeatures.forEach(function (_a) {
-                var code = _a.code, data = _a.data;
+        lengthOnRef = readLength;
+        if (readFeatures) {
+            for (const { code, data } of readFeatures) {
                 if (code === 'D' || code === 'N') {
-                    lengthOnRef_1 += data;
+                    lengthOnRef += data;
                 }
                 else if (code === 'I' || code === 'S') {
-                    lengthOnRef_1 -= data.length;
+                    lengthOnRef = lengthOnRef - data.length;
                 }
                 else if (code === 'i') {
-                    lengthOnRef_1 -= 1;
+                    lengthOnRef = lengthOnRef - 1;
                 }
-            });
+            }
         }
-        if (Number.isNaN(lengthOnRef_1)) {
-            console.warn("".concat(cramRecord.readName ||
-                "".concat(cramRecord.sequenceId, ":").concat(cramRecord.alignmentStart), " record has invalid read features"));
-            lengthOnRef_1 = cramRecord.readLength;
+        if (Number.isNaN(lengthOnRef)) {
+            console.warn(`${readName || `${sequenceId}:${alignmentStart}`} record has invalid read features`);
+            lengthOnRef = readLength;
         }
-        cramRecord.lengthOnRef = lengthOnRef_1;
         // mapping quality
-        cramRecord.mappingQuality = decodeDataSeries('MQ');
-        if (cramRecord.isPreservingQualityScores()) {
-            var bases = new Array(cramRecord.readLength);
-            for (var i = 0; i < bases.length; i += 1) {
-                bases[i] = decodeDataSeries('QS');
+        mappingQuality = decodeDataSeries('MQ');
+        if (record_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
+            qualityScores = new Array(readLength);
+            for (let i = 0; i < qualityScores.length; i++) {
+                qualityScores[i] = decodeDataSeries('QS');
             }
-            cramRecord.qualityScores = bases;
         }
     }
-    else if (cramRecord.isUnknownBases()) {
-        cramRecord.readBases = null;
-        cramRecord.qualityScores = null;
+    else if (record_1.CramFlagsDecoder.isDecodeSequenceAsStar(cramFlags)) {
+        readBases = null;
+        qualityScores = null;
     }
     else {
-        var bases = new Array(cramRecord.readLength);
-        for (var i = 0; i < bases.length; i += 1) {
+        const bases = new Array(readLength);
+        for (let i = 0; i < bases.length; i += 1) {
             bases[i] = decodeDataSeries('BA');
         }
-        cramRecord.readBases = String.fromCharCode.apply(String, bases);
-        if (cramRecord.isPreservingQualityScores()) {
-            for (var i = 0; i < bases.length; i += 1) {
-                bases[i] = decodeDataSeries('QS');
+        readBases = String.fromCharCode(...bases);
+        if (record_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
+            qualityScores = new Array(readLength);
+            for (let i = 0; i < bases.length; i += 1) {
+                qualityScores[i] = decodeDataSeries('QS');
             }
-            cramRecord.qualityScores = bases;
         }
     }
-    return cramRecord;
+    return {
+        readLength,
+        sequenceId,
+        cramFlags,
+        flags,
+        alignmentStart,
+        readGroupId,
+        readName,
+        mateToUse,
+        templateSize,
+        mateRecordNumber,
+        readFeatures,
+        lengthOnRef,
+        mappingQuality,
+        qualityScores,
+        readBases,
+        tags,
+    };
 }
 exports.default = decodeRecord;
 //# sourceMappingURL=decodeRecord.js.map

package/dist/cramFile/slice/decodeRecord.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/index.d.ts

@@ -1,20 +1,27 @@
+import CramRecord from '../record';
+import CramContainer from '../container';
+import { CramFileBlock } from '../file';
+import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
+export declare type SliceHeader = CramFileBlock & {
+    parsedContent: MappedSliceHeader | UnmappedSliceHeader;
+};
 export default class CramSlice {
-    constructor(container: any, position: any);
-    container: any;
-    file: any;
-    containerPosition: any;
-    getHeader(): Promise<any>;
-    getBlocks(): Promise<any[]>;
-    getCoreDataBlock(): Promise<any>;
-    _getBlocksContentIdIndex(): Promise<{}>;
-    getBlockByContentId(id: any): Promise<any>;
+    container: CramContainer;
+    containerPosition: number;
+    private file;
+    constructor(container: CramContainer, containerPosition: number, _unused: number);
+    getHeader(): Promise<SliceHeader>;
+    getBlocks(): Promise<CramFileBlock[]>;
+    getCoreDataBlock(): Promise<CramFileBlock>;
+    _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
+    getBlockByContentId(id: number): Promise<CramFileBlock>;
     getReferenceRegion(): Promise<{
         seq: any;
-        start: any;
+        start: number;
         end: number;
-        span: any;
+        span: number;
     } | undefined>;
-    getAllRecords(): Promise<any>;
-    _fetchRecords(): Promise<any[]>;
-    getRecords(filterFunction: any): Promise<any>;
+    getAllRecords(): Promise<CramRecord[]>;
+    _fetchRecords(): Promise<CramRecord[]>;
+    getRecords(filterFunction: (r: CramRecord) => boolean): Promise<CramRecord[]>;
 }