@gmod/cram 1.6.3 → 1.7.0

package/dist/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/dist/cramFile/sectionParsers.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSectionParsers = exports.cramFileDefinition = void 0;
-var binary_parser_1 = require("@gmod/binary-parser");
-var singleItf8 = new binary_parser_1.Parser().itf8();
-var cramFileDefinition = {
+exports.getSectionParsers = exports.cramFileDefinition = exports.isMappedSliceHeader = void 0;
+const binary_parser_1 = require("@gmod/binary-parser");
+const singleItf8 = new binary_parser_1.Parser().itf8();
+const cramFileDefinition = {
     parser: new binary_parser_1.Parser()
         .string('magic', { length: 4 })
         .uint8('majorVersion')
@@ -12,11 +12,11 @@ var cramFileDefinition = {
     maxLength: 26,
 };
 exports.cramFileDefinition = cramFileDefinition;
-var cramBlockHeader = {
+const cramBlockHeader = {
     parser: new binary_parser_1.Parser()
         .uint8('compressionMethod', {
-        formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ b) {
-            var method = [
+        formatter: /* istanbul ignore next */ /* istanbul ignore next */ b => {
+            const method = [
                 'raw',
                 'gzip',
                 'bzip2',
@@ -28,14 +28,14 @@ var cramBlockHeader = {
                 'tok3',
             ][b];
             if (!method) {
-                throw new Error("compression method number ".concat(b, " not implemented"));
+                throw new Error(`compression method number ${b} not implemented`);
             }
             return method;
         },
     })
         .uint8('contentType', {
-        formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ b) {
-            var type = [
+        formatter: /* istanbul ignore next */ /* istanbul ignore next */ b => {
+            const type = [
                 'FILE_HEADER',
                 'COMPRESSION_HEADER',
                 'MAPPED_SLICE_HEADER',
@@ -44,7 +44,7 @@ var cramBlockHeader = {
                 'CORE_DATA',
             ][b];
             if (!type) {
-                throw new Error("invalid block content type id ".concat(b));
+                throw new Error(`invalid block content type id ${b}`);
             }
             return type;
         },
@@ -54,30 +54,18 @@ var cramBlockHeader = {
         .itf8('uncompressedSize'),
     maxLength: 17,
 };
-var cramBlockCrc32 = {
+const cramBlockCrc32 = {
     parser: new binary_parser_1.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
-// ]
-var cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents', {
+const cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents', {
     length: 'size',
-    formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ buffer) {
+    formatter: /* istanbul ignore next */ /* istanbul ignore next */ buffer => {
         function makeTagSet(stringStart, stringEnd) {
-            var str = buffer.toString('utf8', stringStart, stringEnd);
-            var tags = [];
-            for (var i_1 = 0; i_1 < str.length; i_1 += 3) {
-                tags.push(str.substr(i_1, 3));
+            const str = buffer.toString('utf8', stringStart, stringEnd);
+            const tags = [];
+            for (let i = 0; i < str.length; i += 3) {
+                tags.push(str.substr(i, 3));
             }
             return tags;
         }
@@ -99,10 +87,10 @@ var cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents',
     },
 });
 // const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
-var parseByteAsBool = new binary_parser_1.Parser().uint8(null, {
-    formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ val) { return !!val; },
+const parseByteAsBool = new binary_parser_1.Parser().uint8(null, {
+    formatter: /* istanbul ignore next */ /* istanbul ignore next */ val => !!val,
 });
-var cramPreservationMap = new binary_parser_1.Parser()
+const cramPreservationMap = new binary_parser_1.Parser()
     .itf8('mapSize')
     .itf8('mapCount')
     .array('ents', {
@@ -125,35 +113,39 @@ var cramPreservationMap = new binary_parser_1.Parser()
             SM: new binary_parser_1.Parser().array(null, { type: 'uint8', length: 5 }),
             TD: new binary_parser_1.Parser().nest(null, {
                 type: cramTagDictionary,
-                formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ data) { return data.ents; },
+                formatter: /* istanbul ignore next */ /* istanbul ignore next */ data => data.ents,
             }),
         },
     }),
 });
 /* istanbul ignore next */
 function formatMap(data) {
-    var map = {};
-    for (var i = 0; i < data.ents.length; i += 1) {
-        var _a = data.ents[i], key = _a.key, value = _a.value;
+    const map = {};
+    for (let i = 0; i < data.ents.length; i += 1) {
+        const { key, value } = data.ents[i];
         if (map[key]) {
-            console.warn("duplicate key ".concat(key, " in map"));
+            console.warn(`duplicate key ${key} in map`);
         }
         map[key] = value;
     }
     return map;
 }
-var unversionedParsers = {
-    cramFileDefinition: cramFileDefinition,
-    cramBlockHeader: cramBlockHeader,
-    cramBlockCrc32: cramBlockCrc32,
+const unversionedParsers = {
+    cramFileDefinition,
+    cramBlockHeader,
+    cramBlockCrc32,
 };
+function isMappedSliceHeader(header) {
+    return typeof header.refSeqId === 'number';
+}
+exports.isMappedSliceHeader = isMappedSliceHeader;
 // each of these is a function of the major and minor version
-var versionedParsers = {
+const versionedParsers = {
     // assemble a section parser for the unmapped slice header, with slight
     // variations depending on the major version of the cram file
-    cramUnmappedSliceHeader: function (majorVersion) {
-        var maxLength = 0;
-        var parser = new binary_parser_1.Parser().itf8('numRecords');
+    cramUnmappedSliceHeader(majorVersion) {
+        let maxLength = 0;
+        let parser = new binary_parser_1.Parser().itf8('numRecords');
         maxLength += 5;
         // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
         if (majorVersion >= 3) {
@@ -177,18 +169,18 @@ var versionedParsers = {
             parser = parser.array('md5', { type: 'uint8', length: 16 });
             maxLength += 16;
         }
-        var maxLengthFunc = function (numContentIds) { return maxLength + numContentIds * 5; };
-        return { parser: parser, maxLength: maxLengthFunc }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
+        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
     // variations depending on the major version of the cram file
-    cramMappedSliceHeader: function (majorVersion) {
-        var parser = new binary_parser_1.Parser()
+    cramMappedSliceHeader(majorVersion) {
+        let parser = new binary_parser_1.Parser()
             .itf8('refSeqId')
             .itf8('refSeqStart')
             .itf8('refSeqSpan')
             .itf8('numRecords');
-        var maxLength = 5 * 4;
+        let maxLength = 5 * 4;
         if (majorVersion >= 3) {
             parser = parser.ltf8('recordCounter');
             maxLength += 9;
@@ -211,11 +203,11 @@ var versionedParsers = {
             parser = parser.array('md5', { type: 'uint8', length: 16 });
             maxLength += 16;
         }
-        var maxLengthFunc = function (numContentIds) { return maxLength + numContentIds * 5; };
-        return { parser: parser, maxLength: maxLengthFunc };
+        const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
+        return { parser, maxLength: maxLengthFunc };
     },
-    cramEncoding: function (majorVersion) {
-        var parser = new binary_parser_1.Parser()
+    cramEncoding(majorVersion) {
+        const parser = new binary_parser_1.Parser()
             .namely('cramEncoding')
             .itf8('codecId')
             .itf8('parametersBytes')
@@ -235,17 +227,16 @@ var versionedParsers = {
                     .nest('lengthsEncoding', { type: 'cramEncoding' })
                     .nest('valuesEncoding', { type: 'cramEncoding' }),
                 // BYTE_ARRAY_STOP is a little different for CRAM v1
-                5: new binary_parser_1.Parser()
-                    .uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
+                5: new binary_parser_1.Parser().uint8('stopByte').itf8('blockContentId'),
                 6: new binary_parser_1.Parser().itf8('offset').itf8('length'),
                 7: new binary_parser_1.Parser().itf8('offset').itf8('K'),
                 8: new binary_parser_1.Parser().itf8('offset').itf8('log2m'),
                 9: new binary_parser_1.Parser().itf8('offset'), // GAMMA
             },
         });
-        return { parser: parser };
+        return { parser };
     },
-    cramDataSeriesEncodingMap: function (majorVersion) {
+    cramDataSeriesEncodingMap(majorVersion) {
         return new binary_parser_1.Parser()
             .itf8('mapSize')
             .itf8('mapCount')
@@ -256,7 +247,7 @@ var versionedParsers = {
                 .nest('value', { type: this.cramEncoding(majorVersion).parser }),
         });
     },
-    cramTagEncodingMap: function (majorVersion) {
+    cramTagEncodingMap(majorVersion) {
         return new binary_parser_1.Parser()
             .itf8('mapSize')
             .itf8('mapCount')
@@ -264,18 +255,17 @@ var versionedParsers = {
             length: 'mapCount',
             type: new binary_parser_1.Parser()
                 .itf8('key', {
-                formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ integerRepresentation) {
-                    /* istanbul ignore next */
-                    return String.fromCharCode((integerRepresentation >> 16) & 0xff) +
-                        String.fromCharCode((integerRepresentation >> 8) & 0xff) +
-                        String.fromCharCode(integerRepresentation & 0xff);
-                },
+                formatter: /* istanbul ignore next */ /* istanbul ignore next */ integerRepresentation => 
+                /* istanbul ignore next */
+                String.fromCharCode((integerRepresentation >> 16) & 0xff) +
+                    String.fromCharCode((integerRepresentation >> 8) & 0xff) +
+                    String.fromCharCode(integerRepresentation & 0xff),
             })
                 .nest('value', { type: this.cramEncoding(majorVersion).parser }),
         });
     },
-    cramCompressionHeader: function (majorVersion) {
-        var parser = new binary_parser_1.Parser();
+    cramCompressionHeader(majorVersion) {
+        let parser = new binary_parser_1.Parser();
         // TODO: if we want to support CRAM v1, we will need to refactor
         // compression header into 2 parts to parse the landmarks,
         // like the container header
@@ -292,16 +282,16 @@ var versionedParsers = {
             type: this.cramTagEncodingMap(majorVersion),
             formatter: formatMap,
         });
-        return { parser: parser };
+        return { parser };
     },
-    cramContainerHeader1: function (majorVersion) {
-        var parser = new binary_parser_1.Parser()
+    cramContainerHeader1(majorVersion) {
+        let parser = new binary_parser_1.Parser()
             .int32('length') // byte size of the container data (blocks)
             .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
             .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
             .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
             .itf8('numRecords'); // number of records in the container
-        var maxLength = 4 + 5 * 4;
+        let maxLength = 4 + 5 * 4;
         if (majorVersion >= 3) {
             parser = parser.ltf8('recordCounter'); // 1-based sequential index of records in the file/stream.
             maxLength += 9;
@@ -318,10 +308,10 @@ var versionedParsers = {
             .itf8('numBlocks') // the number of blocks
             .itf8('numLandmarks'); // the number of landmarks
         maxLength += 5 + 5;
-        return { parser: parser, maxLength: maxLength };
+        return { parser, maxLength };
     },
-    cramContainerHeader2: function (majorVersion) {
-        var parser = new binary_parser_1.Parser()
+    cramContainerHeader2(majorVersion) {
+        let parser = new binary_parser_1.Parser()
             .itf8('numLandmarks') // the number of blocks
             // Each integer value of this array is a byte offset
             // into the blocks byte array. Landmarks are used for
@@ -330,20 +320,20 @@ var versionedParsers = {
             type: new binary_parser_1.Parser().itf8(),
             length: 'numLandmarks',
         });
-        var crcLength = 0;
+        let crcLength = 0;
         if (majorVersion >= 3) {
             parser = parser.uint32('crc32');
             crcLength = 4;
         }
         return {
-            parser: parser,
-            maxLength: function (numLandmarks) { return 5 + numLandmarks * 5 + crcLength; },
+            parser,
+            maxLength: (numLandmarks) => 5 + numLandmarks * 5 + crcLength,
         };
     },
 };
 function getSectionParsers(majorVersion) {
-    var parsers = Object.assign({}, unversionedParsers);
-    Object.keys(versionedParsers).forEach(function (parserName) {
+    const parsers = Object.assign({}, unversionedParsers);
+    Object.keys(versionedParsers).forEach(parserName => {
         parsers[parserName] = versionedParsers[parserName](majorVersion);
     });
     return parsers;

package/dist/cramFile/sectionParsers.js.map

@@ -1 +1 @@
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package/dist/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>;
+};