@gmod/cram 1.5.9 → 1.6.2

package/esm/cramFile/sectionParsers.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/slice/decodeRecord.d.ts

@@ -0,0 +1,2 @@
+export default function decodeRecord(slice: any, decodeDataSeries: any, compressionScheme: any, sliceHeader: any, coreDataBlock: any, blocksByContentId: any, cursors: any, majorVersion: any, recordNumber: any): CramRecord;
+import CramRecord from "../record";

package/esm/cramFile/slice/decodeRecord.js

@@ -0,0 +1,299 @@
+import Long from 'long';
+import { CramMalformedError, CramUnimplementedError } from '../../errors';
+import CramRecord from '../record';
+import Constants from '../constants';
+/**
+ * given a Buffer, read a string up to the first null character
+ * @private
+ */
+function readNullTerminatedStringFromBuffer(buffer) {
+    const zeroOffset = buffer.indexOf(0);
+    if (zeroOffset === -1) {
+        return buffer.toString('utf8');
+    }
+    return buffer.toString('utf8', 0, zeroOffset);
+}
+/**
+ * parse a BAM tag's array value from a binary buffer
+ * @private
+ */
+function parseTagValueArray(buffer) {
+    const arrayType = String.fromCharCode(buffer[0]);
+    const length = buffer.readInt32LE(1);
+    const schema = {
+        c: ['readInt8', 1],
+        C: ['readUInt8', 1],
+        s: ['readInt16LE', 2],
+        S: ['readUInt16LE', 2],
+        i: ['readInt32LE', 4],
+        I: ['readUInt32LE', 4],
+        f: ['readFloatLE', 4],
+    }[arrayType];
+    if (!schema) {
+        throw new CramMalformedError(`invalid tag value array type '${arrayType}'`);
+    }
+    const [getMethod, itemSize] = schema;
+    const array = new Array(length);
+    let offset = 5;
+    for (let i = 0; i < length; i += 1) {
+        array[i] = buffer[getMethod](offset);
+        offset += itemSize;
+    }
+    return array;
+}
+function parseTagData(tagType, buffer) {
+    if (!buffer.readInt32LE) {
+        buffer = Buffer.from(buffer);
+    }
+    if (tagType === 'Z') {
+        return readNullTerminatedStringFromBuffer(buffer);
+    }
+    if (tagType === 'A') {
+        return String.fromCharCode(buffer[0]);
+    }
+    if (tagType === 'I') {
+        const val = Long.fromBytesLE(buffer);
+        if (val.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            val.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new CramUnimplementedError('integer overflow');
+        }
+        return val.toNumber();
+    }
+    if (tagType === 'i') {
+        return buffer.readInt32LE(0);
+    }
+    if (tagType === 's') {
+        return buffer.readInt16LE(0);
+    }
+    if (tagType === 'S') {
+        return buffer.readUInt16LE(0);
+    }
+    if (tagType === 'c') {
+        return buffer.readInt8(0);
+    }
+    if (tagType === 'C') {
+        return buffer.readUInt8(0);
+    }
+    if (tagType === 'f') {
+        return buffer.readFloatLE(0);
+    }
+    if (tagType === 'H') {
+        const hex = readNullTerminatedStringFromBuffer(buffer);
+        return Number.parseInt(hex.replace(/^0x/, ''), 16);
+    }
+    if (tagType === 'B') {
+        return parseTagValueArray(buffer);
+    }
+    throw new CramMalformedError(`Unrecognized tag type ${tagType}`);
+}
+function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
+    let currentReadPos = 0;
+    let currentRefPos = cramRecord.alignmentStart - 1;
+    const readFeatures = new Array(readFeatureCount);
+    function decodeRFData([type, dataSeriesName]) {
+        const data = decodeDataSeries(dataSeriesName);
+        if (type === 'character') {
+            return String.fromCharCode(data);
+        }
+        if (type === 'string') {
+            return data.toString('utf8');
+        }
+        if (type === 'numArray') {
+            return data.toArray();
+        }
+        // else if (type === 'number') {
+        //   return data[0]
+        // }
+        return data;
+    }
+    for (let i = 0; i < readFeatureCount; i += 1) {
+        const code = String.fromCharCode(decodeDataSeries('FC'));
+        const readPosDelta = decodeDataSeries('FP');
+        const readFeature = { code };
+        // map of operator name -> data series name
+        const data1Schema = {
+            B: ['character', 'BA'],
+            S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
+            X: ['number', 'BS'],
+            D: ['number', 'DL'],
+            I: ['string', 'IN'],
+            i: ['character', 'BA'],
+            b: ['string', 'BB'],
+            q: ['numArray', 'QQ'],
+            Q: ['number', 'QS'],
+            H: ['number', 'HC'],
+            P: ['number', 'PD'],
+            N: ['number', 'RS'],
+        }[code];
+        if (!data1Schema) {
+            throw new CramMalformedError(`invalid read feature code "${code}"`);
+        }
+        readFeature.data = decodeRFData(data1Schema);
+        // if this is a tag with two data items, make the data an array and add the second item
+        const data2Schema = { B: ['number', 'QS'] }[code];
+        if (data2Schema) {
+            readFeature.data = [readFeature.data, decodeRFData(data2Schema)];
+        }
+        currentReadPos += readPosDelta;
+        readFeature.pos = currentReadPos;
+        currentRefPos += readPosDelta;
+        readFeature.refPos = currentRefPos;
+        // for gapping features, adjust the reference position for read features that follow
+        if (code === 'D' || code === 'N') {
+            currentRefPos += readFeature.data;
+        }
+        else if (code === 'I' || code === 'S') {
+            currentRefPos -= readFeature.data.length;
+        }
+        else if (code === 'i') {
+            currentRefPos -= 1;
+        }
+        readFeatures[i] = readFeature;
+    }
+    return readFeatures;
+}
+function thingToString(thing) {
+    if (thing instanceof Buffer) {
+        return readNullTerminatedStringFromBuffer(thing);
+    }
+    if (thing.length && thing.indexOf) {
+        // array-like
+        if (!thing[thing.length - 1]) {
+            // trim zeroes off the end if necessary
+            const termIndex = thing.indexOf(0);
+            return String.fromCharCode(...thing.slice(0, termIndex));
+        }
+        return String.fromCharCode(...thing);
+    }
+    return String(thing);
+}
+export default function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
+    const cramRecord = new CramRecord();
+    cramRecord.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');
+    }
+    else {
+        cramRecord.sequenceId = sliceHeader.content.refSeqId;
+    }
+    cramRecord.readLength = decodeDataSeries('RL');
+    // if APDelta, will calculate the true start in a second pass
+    cramRecord.alignmentStart = decodeDataSeries('AP');
+    if (compressionScheme.APdelta) {
+        cramRecord.alignmentStart += cursors.lastAlignmentStart;
+    }
+    cursors.lastAlignmentStart = cramRecord.alignmentStart;
+    cramRecord.readGroupId = decodeDataSeries('RG');
+    if (compressionScheme.readNamesIncluded) {
+        cramRecord.readName = thingToString(decodeDataSeries('RN'));
+    }
+    // mate record
+    if (cramRecord.isDetached()) {
+        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
+        const mate = {};
+        mate.flags = decodeDataSeries('MF');
+        if (!compressionScheme.readNamesIncluded) {
+            mate.readName = thingToString(decodeDataSeries('RN'));
+            cramRecord.readName = mate.readName;
+        }
+        mate.sequenceId = decodeDataSeries('NS');
+        mate.alignmentStart = decodeDataSeries('NP');
+        if (mate.flags || mate.sequenceId > -1) {
+            cramRecord.mate = mate;
+        }
+        cramRecord.templateSize = decodeDataSeries('TS');
+        // set mate unmapped if needed
+        if (mate.flags & Constants.CRAM_M_UNMAP) {
+            cramRecord.flags |= Constants.BAM_FMUNMAP;
+        }
+        // set mate reversed if needed
+        if (mate.flags & Constants.CRAM_M_REVERSE) {
+            cramRecord.flags |= Constants.BAM_FMREVERSE;
+        }
+        // detachedCount++
+    }
+    else if (cramRecord.hasMateDownStream()) {
+        cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
+    }
+    // TODO: the aux tag parsing will have to be refactored if we want to support
+    // cram v1
+    const TLindex = decodeDataSeries('TL');
+    if (TLindex < 0) {
+        /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
+        throw new CramMalformedError('invalid TL index');
+    }
+    // TN = tag names
+    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 CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);
+        }
+        const tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        cramRecord.tags[tagName] = parseTagData(tagType, tagData);
+    }
+    if (!cramRecord.isSegmentUnmapped()) {
+        // reading read features
+        const /* int */ readFeatureCount = decodeDataSeries('FN');
+        if (readFeatureCount) {
+            cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
+        }
+        // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+        let lengthOnRef = cramRecord.readLength;
+        if (cramRecord.readFeatures) {
+            cramRecord.readFeatures.forEach(({ code, data }) => {
+                if (code === 'D' || code === 'N') {
+                    lengthOnRef += data;
+                }
+                else if (code === 'I' || code === 'S') {
+                    lengthOnRef -= data.length;
+                }
+                else if (code === 'i') {
+                    lengthOnRef -= 1;
+                }
+            });
+        }
+        if (Number.isNaN(lengthOnRef)) {
+            console.warn(`${cramRecord.readName ||
+                `${cramRecord.sequenceId}:${cramRecord.alignmentStart}`} record has invalid read features`);
+            lengthOnRef = cramRecord.readLength;
+        }
+        cramRecord.lengthOnRef = lengthOnRef;
+        // mapping quality
+        cramRecord.mappingQuality = decodeDataSeries('MQ');
+        if (cramRecord.isPreservingQualityScores()) {
+            const bases = new Array(cramRecord.readLength);
+            for (let i = 0; i < bases.length; i += 1) {
+                bases[i] = decodeDataSeries('QS');
+            }
+            cramRecord.qualityScores = bases;
+        }
+    }
+    else if (cramRecord.isUnknownBases()) {
+        cramRecord.readBases = null;
+        cramRecord.qualityScores = null;
+    }
+    else {
+        const bases = new Array(cramRecord.readLength);
+        for (let i = 0; i < bases.length; i += 1) {
+            bases[i] = decodeDataSeries('BA');
+        }
+        cramRecord.readBases = String.fromCharCode(...bases);
+        if (cramRecord.isPreservingQualityScores()) {
+            for (let i = 0; i < bases.length; i += 1) {
+                bases[i] = decodeDataSeries('QS');
+            }
+            cramRecord.qualityScores = bases;
+        }
+    }
+    return cramRecord;
+}
+//# sourceMappingURL=decodeRecord.js.map

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

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package/esm/cramFile/slice/index.d.ts

@@ -0,0 +1,20 @@
+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>;
+    getReferenceRegion(): Promise<{
+        seq: any;
+        start: any;
+        end: number;
+        span: any;
+    } | undefined>;
+    getAllRecords(): Promise<any>;
+    _fetchRecords(): Promise<any[]>;
+    getRecords(filterFunction: any): Promise<any>;
+}