@gmod/cram 1.6.3 → 1.7.0

package/esm/cramFile/record.js.map

@@ -1 +1 @@
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package/esm/cramFile/sectionParsers.d.ts

@@ -1,18 +1,109 @@
-export namespace cramFileDefinition {
-    const parser: any;
-    const maxLength: number;
-}
-export function getSectionParsers(majorVersion: any): {
+import { Parser } from '@gmod/binary-parser';
+import { TupleOf } from '../typescript';
+import { ParsedItem } from './util';
+import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
+import { CramEncoding } from './encoding';
+declare const cramFileDefinition: {
+    parser: Parser<unknown>;
+    maxLength: number;
+};
+export declare type CramTagDictionary = string[][];
+export declare type CramPreservationMap = {
+    MI: boolean;
+    UI: boolean;
+    PI: boolean;
+    RN: boolean;
+    AP: boolean;
+    RR: boolean;
+    SM: [number, number, number, number, number];
+    TD: CramTagDictionary;
+};
+export declare type MappedSliceHeader = {
+    refSeqId: number;
+    refSeqStart: number;
+    refSeqSpan: number;
+    numRecords: number;
+    recordCounter: number;
+    numBlocks: number;
+    numContentIds: number;
+    contentIds: number[];
+    refBaseBlockId: number;
+    md5: TupleOf<number, 16>;
+};
+export declare type UnmappedSliceHeader = {
+    numRecords: number;
+    recordCounter: number;
+    numBlocks: number;
+    numContentIds: number;
+    contentIds: number[];
+    md5: TupleOf<number, 16>;
+};
+export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
+export declare type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
+export declare type BlockHeader = {
+    compressionMethod: CompressionMethod;
+    contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';
+    contentId: number;
+    compressedSize: number;
+    uncompressedSize: number;
+};
+export declare type CramCompressionHeader = ParsedItem<{
+    preservation: CramPreservationMap;
+    dataSeriesEncoding: DataSeriesEncodingMap;
+    tagEncoding: Record<string, CramEncoding>;
+}>;
+declare function getSectionParsers(majorVersion: number): {
     cramFileDefinition: {
-        parser: any;
+        parser: Parser<{
+            magic: string;
+            majorVersion: number;
+            minorVersion: number;
+            fileId: string;
+        }>;
         maxLength: number;
     };
+    cramContainerHeader1: {
+        parser: Parser<{
+            length: number;
+            refSeqId: number;
+            refSeqStart: number;
+            alignmentSpan: number;
+            numRecords: number;
+            recordCounter: number;
+            numBases: number;
+            numBlocks: number;
+            numLandmarks: number;
+        }>;
+        maxLength: number;
+    };
+    cramContainerHeader2: {
+        parser: Parser<{
+            numLandmarks: number;
+            landmarks: number[];
+            crc32: number;
+        }>;
+        maxLength: (x: number) => number;
+    };
     cramBlockHeader: {
-        parser: any;
+        parser: Parser<BlockHeader>;
         maxLength: number;
     };
     cramBlockCrc32: {
-        parser: any;
+        parser: Parser<{
+            crc32: number;
+        }>;
         maxLength: number;
     };
+    cramCompressionHeader: {
+        parser: Parser<CramCompressionHeader>;
+    };
+    cramMappedSliceHeader: {
+        parser: Parser<MappedSliceHeader>;
+        maxLength: (numContentIds: number) => number;
+    };
+    cramUnmappedSliceHeader: {
+        parser: Parser<UnmappedSliceHeader>;
+        maxLength: (numContentIds: number) => number;
+    };
 };
+export { cramFileDefinition, getSectionParsers };

package/esm/cramFile/sectionParsers.js

@@ -54,18 +54,6 @@ const cramBlockCrc32 = {
     parser: new Parser().uint32('crc32'),
     maxLength: 4,
 };
-// const ENCODING_NAMES = [
-//   'NULL', // 0
-//   'EXTERNAL', // 1
-//   'GOLOMB', // 2
-//   'HUFFMAN_INT', // 3
-//   'BYTE_ARRAY_LEN', // 4
-//   'BYTE_ARRAY_STOP', // 5
-//   'BETA', // 6
-//   'SUBEXP', // 7
-//   'GOLOMB_RICE', // 8
-//   'GAMMA', // 9
-// ]
 const cramTagDictionary = new Parser().itf8('size').buffer('ents', {
     length: 'size',
     formatter: /* istanbul ignore next */ /* istanbul ignore next */ buffer => {
@@ -143,6 +131,9 @@ const unversionedParsers = {
     cramBlockHeader,
     cramBlockCrc32,
 };
+export function isMappedSliceHeader(header) {
+    return typeof header.refSeqId === 'number';
+}
 // each of these is a function of the major and minor version
 const versionedParsers = {
     // assemble a section parser for the unmapped slice header, with slight
@@ -173,7 +164,7 @@ const versionedParsers = {
             parser = parser.array('md5', { type: 'uint8', length: 16 });
             maxLength += 16;
         }
-        const maxLengthFunc = numContentIds => maxLength + numContentIds * 5;
+        const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
         return { parser, maxLength: maxLengthFunc }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
     },
     // assembles a section parser for the unmapped slice header, with slight
@@ -207,7 +198,7 @@ const versionedParsers = {
             parser = parser.array('md5', { type: 'uint8', length: 16 });
             maxLength += 16;
         }
-        const maxLengthFunc = numContentIds => maxLength + numContentIds * 5;
+        const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
         return { parser, maxLength: maxLengthFunc };
     },
     cramEncoding(majorVersion) {
@@ -231,8 +222,7 @@ const versionedParsers = {
                     .nest('lengthsEncoding', { type: 'cramEncoding' })
                     .nest('valuesEncoding', { type: 'cramEncoding' }),
                 // BYTE_ARRAY_STOP is a little different for CRAM v1
-                5: new Parser()
-                    .uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
+                5: new Parser().uint8('stopByte').itf8('blockContentId'),
                 6: new Parser().itf8('offset').itf8('length'),
                 7: new Parser().itf8('offset').itf8('K'),
                 8: new Parser().itf8('offset').itf8('log2m'),
@@ -332,7 +322,7 @@ const versionedParsers = {
         }
         return {
             parser,
-            maxLength: numLandmarks => 5 + numLandmarks * 5 + crcLength,
+            maxLength: (numLandmarks) => 5 + numLandmarks * 5 + crcLength,
         };
     },
 };

package/esm/cramFile/sectionParsers.js.map

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

@@ -1,2 +1,30 @@
-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";
+import { ReadFeature } from '../record';
+import CramSlice, { SliceHeader } from './index';
+import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme';
+import { CramFileBlock } from '../file';
+import { Cursors, DataTypeMapping } from '../codecs/_base';
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
+export declare type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
+export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
+    readLength: number;
+    sequenceId: number;
+    cramFlags: number;
+    flags: number;
+    alignmentStart: number;
+    readGroupId: number;
+    readName: string | undefined;
+    mateToUse: {
+        mateFlags: number;
+        mateSequenceId: number;
+        mateAlignmentStart: number;
+        mateReadName: string | undefined;
+    } | undefined;
+    templateSize: number | undefined;
+    mateRecordNumber: number | undefined;
+    readFeatures: ReadFeature[] | undefined;
+    lengthOnRef: number | undefined;
+    mappingQuality: number | undefined;
+    qualityScores: number[] | null | undefined;
+    readBases: string | null | undefined;
+    tags: Record<string, any>;
+};

package/esm/cramFile/slice/decodeRecord.js

@@ -1,7 +1,7 @@
 import Long from 'long';
 import { CramMalformedError } from '../../errors';
-import CramRecord from '../record';
-import Constants from '../constants';
+import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from '../record';
+import { isMappedSliceHeader } from '../sectionParsers';
 /**
  * given a Buffer, read a string up to the first null character
  * @private
@@ -105,9 +105,9 @@ function parseTagData(tagType, buffer) {
     }
     throw new CramMalformedError(`Unrecognized tag type ${tagType}`);
 }
-function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
+function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
     let currentReadPos = 0;
-    let currentRefPos = cramRecord.alignmentStart - 1;
+    let currentRefPos = alignmentStart - 1;
     const readFeatures = new Array(readFeatureCount);
     function decodeRFData([type, dataSeriesName]) {
         const data = decodeDataSeries(dataSeriesName);
@@ -128,7 +128,6 @@ function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, comp
     for (let i = 0; i < readFeatureCount; i += 1) {
         const code = String.fromCharCode(decodeDataSeries('FC'));
         const readPosDelta = decodeDataSeries('FP');
-        const readFeature = { code };
         // map of operator name -> data series name
         const data1Schema = {
             B: ['character', 'BA'],
@@ -147,81 +146,94 @@ function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, comp
         if (!data1Schema) {
             throw new CramMalformedError(`invalid read feature code "${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
         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;
 }
 export default function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
-    const cramRecord = new CramRecord();
-    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 (!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 (CramFlagsDecoder.isDetached(cramFlags)) {
         // 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');
+        // 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.CRAM_M_UNMAP) {
-            cramRecord.flags |= Constants.BAM_FMUNMAP;
+        if (MateFlagsDecoder.isUnmapped(mateFlags)) {
+            flags = BamFlagsDecoder.setMateUnmapped(flags);
         }
         // set mate reversed if needed
-        if (mate.flags & Constants.CRAM_M_REVERSE) {
-            cramRecord.flags |= Constants.BAM_FMREVERSE;
+        if (MateFlagsDecoder.isOnNegativeStrand(mateFlags)) {
+            flags = BamFlagsDecoder.setMateReverseComplemented(flags);
         }
         // detachedCount++
     }
-    else if (cramRecord.hasMateDownStream()) {
-        cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
+    else if (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
@@ -230,6 +242,7 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
         /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
         throw new CramMalformedError('invalid TL index');
     }
+    const tags = {};
     // TN = tag names
     const TN = compressionScheme.getTagNames(TLindex);
     const ntags = TN.length;
@@ -242,62 +255,81 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
             throw new CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);
         }
         const tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-        cramRecord.tags[tagName] = parseTagData(tagType, tagData);
-    }
-    if (!cramRecord.isSegmentUnmapped()) {
+        tags[tagName] = parseTagData(tagType, tagData);
+    }
+    let readFeatures;
+    let lengthOnRef;
+    let mappingQuality;
+    let qualityScores;
+    let readBases = undefined;
+    if (!BamFlagsDecoder.isSegmentUnmapped(flags)) {
         // reading read features
-        const /* int */ readFeatureCount = decodeDataSeries('FN');
+        const readFeatureCount = decodeDataSeries('FN');
         if (readFeatureCount) {
-            cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
+            readFeatures = decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
         }
         // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
-        let lengthOnRef = cramRecord.readLength;
-        if (cramRecord.readFeatures) {
-            cramRecord.readFeatures.forEach(({ code, data }) => {
+        lengthOnRef = readLength;
+        if (readFeatures) {
+            for (const { code, data } of readFeatures) {
                 if (code === 'D' || code === 'N') {
                     lengthOnRef += data;
                 }
                 else if (code === 'I' || code === 'S') {
-                    lengthOnRef -= data.length;
+                    lengthOnRef = lengthOnRef - data.length;
                 }
                 else if (code === 'i') {
-                    lengthOnRef -= 1;
+                    lengthOnRef = lengthOnRef - 1;
                 }
-            });
+            }
         }
         if (Number.isNaN(lengthOnRef)) {
-            console.warn(`${cramRecord.readName ||
-                `${cramRecord.sequenceId}:${cramRecord.alignmentStart}`} record has invalid read features`);
-            lengthOnRef = cramRecord.readLength;
+            console.warn(`${readName || `${sequenceId}:${alignmentStart}`} record has invalid read features`);
+            lengthOnRef = 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');
+        mappingQuality = decodeDataSeries('MQ');
+        if (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 (CramFlagsDecoder.isDecodeSequenceAsStar(cramFlags)) {
+        readBases = null;
+        qualityScores = null;
     }
     else {
-        const bases = new Array(cramRecord.readLength);
+        const bases = new Array(readLength);
         for (let i = 0; i < bases.length; i += 1) {
             bases[i] = decodeDataSeries('BA');
         }
-        cramRecord.readBases = String.fromCharCode(...bases);
-        if (cramRecord.isPreservingQualityScores()) {
+        readBases = String.fromCharCode(...bases);
+        if (CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
+            qualityScores = new Array(readLength);
             for (let i = 0; i < bases.length; i += 1) {
-                bases[i] = decodeDataSeries('QS');
+                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,
+    };
 }
 //# sourceMappingURL=decodeRecord.js.map

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