npm - @gmod/cram - Versions diffs - 2.0.0 → 2.0.2 - Mend

@gmod/cram 2.0.0 → 2.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (143) hide show

package/CHANGELOG.md +4 -0
package/dist/craiIndex.d.ts +2 -2
package/dist/craiIndex.js +5 -9
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/_base.d.ts +6 -6
package/dist/cramFile/codecs/beta.js.map +1 -1
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.js +1 -0
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/gamma.js.map +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.d.ts +0 -1
package/dist/cramFile/codecs/huffman.js +1 -3
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/index.js.map +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/compressionScheme.js +1 -1
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/encoding.d.ts +20 -20
package/dist/cramFile/file.d.ts +14 -7
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/filehandle.d.ts +1 -2
package/dist/cramFile/index.d.ts +1 -2
package/dist/cramFile/index.js +3 -3
package/dist/cramFile/index.js.map +1 -1
package/dist/cramFile/record.d.ts +6 -6
package/dist/cramFile/record.js +7 -4
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.d.ts +9 -8
package/dist/cramFile/sectionParsers.js +10 -11
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +7 -11
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js +24 -22
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +1 -0
package/dist/cramFile/util.js +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/index.d.ts +3 -4
package/dist/index.js +7 -30
package/dist/index.js.map +1 -1
package/dist/indexedCramFile.d.ts +6 -6
package/dist/indexedCramFile.js +13 -18
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.d.ts +2 -1
package/dist/io/index.js +4 -3
package/dist/io/index.js.map +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js.map +1 -1
package/dist/sam.d.ts +5 -6
package/dist/sam.js +20 -7
package/dist/sam.js.map +1 -1
package/dist/typescript.js.map +1 -1
package/dist/unzip.d.ts +2 -2
package/dist/unzip.js +1 -1
package/dist/unzip.js.map +1 -1
package/esm/craiIndex.d.ts +2 -2
package/esm/craiIndex.js +5 -9
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/_base.d.ts +6 -6
package/esm/cramFile/codecs/beta.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.js +1 -0
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/gamma.js.map +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.d.ts +0 -1
package/esm/cramFile/codecs/huffman.js +1 -3
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/index.js.map +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/compressionScheme.js +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/encoding.d.ts +20 -20
package/esm/cramFile/file.d.ts +14 -7
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/filehandle.d.ts +1 -2
package/esm/cramFile/index.d.ts +1 -2
package/esm/cramFile/index.js +1 -2
package/esm/cramFile/index.js.map +1 -1
package/esm/cramFile/record.d.ts +6 -6
package/esm/cramFile/record.js +7 -4
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.d.ts +9 -8
package/esm/cramFile/sectionParsers.js +10 -11
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +7 -11
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js +24 -22
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +1 -0
package/esm/cramFile/util.js +1 -1
package/esm/cramFile/util.js.map +1 -1
package/esm/index.d.ts +3 -4
package/esm/index.js +3 -4
package/esm/index.js.map +1 -1
package/esm/indexedCramFile.d.ts +6 -6
package/esm/indexedCramFile.js +13 -18
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.d.ts +2 -1
package/esm/io/index.js +2 -1
package/esm/io/index.js.map +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js.map +1 -1
package/esm/sam.d.ts +5 -6
package/esm/sam.js +20 -7
package/esm/sam.js.map +1 -1
package/esm/typescript.js.map +1 -1
package/esm/unzip.d.ts +2 -2
package/esm/unzip.js +1 -2
package/esm/unzip.js.map +1 -1
package/package.json +11 -11
package/src/craiIndex.ts +8 -13
package/src/cramFile/codecs/_base.ts +3 -3
package/src/cramFile/codecs/external.ts +1 -0
package/src/cramFile/codecs/huffman.ts +7 -8
package/src/cramFile/container/compressionScheme.ts +1 -1
package/src/cramFile/encoding.ts +10 -10
package/src/cramFile/file.ts +5 -5
package/src/cramFile/filehandle.ts +1 -3
package/src/cramFile/index.ts +1 -2
package/src/cramFile/record.ts +13 -10
package/src/cramFile/sectionParsers.ts +8 -9
package/src/cramFile/slice/decodeRecord.ts +15 -17
package/src/cramFile/slice/index.ts +26 -23
package/src/cramFile/util.ts +1 -1
package/src/index.ts +3 -5
package/src/indexedCramFile.ts +19 -23
package/src/io/index.ts +3 -1
package/src/sam.ts +28 -14
package/src/typings/binary-parser.d.ts +1 -1
package/src/unzip.ts +1 -2

package/dist/cramFile/sectionParsers.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 import { Parser } from '@gmod/binary-parser';
 import { TupleOf } from '../typescript';
 import { ParsedItem } from './util';
@@ -8,7 +9,7 @@ declare const cramFileDefinition: {
     maxLength: number;
 };
 export type CramTagDictionary = string[][];
-export type CramPreservationMap = {
+export interface CramPreservationMap {
     MI: boolean;
     UI: boolean;
     PI: boolean;
@@ -17,8 +18,8 @@ export type CramPreservationMap = {
     RR: boolean;
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
-};
-export type MappedSliceHeader = {
+}
+export interface MappedSliceHeader {
     refSeqId: number;
     refSeqStart: number;
     refSeqSpan: number;
@@ -29,24 +30,24 @@ export type MappedSliceHeader = {
     contentIds: number[];
     refBaseBlockId: number;
     md5: TupleOf<number, 16>;
-};
-export type UnmappedSliceHeader = {
+}
+export interface 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 type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
-export type BlockHeader = {
+export interface 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 type CramCompressionHeader = ParsedItem<{
     preservation: CramPreservationMap;
     dataSeriesEncoding: DataSeriesEncodingMap;

package/dist/cramFile/sectionParsers.js CHANGED Viewed

@@ -39,7 +39,7 @@ const cramBlockHeader = {
                 'FILE_HEADER',
                 'COMPRESSION_HEADER',
                 'MAPPED_SLICE_HEADER',
-                'UNMAPPED_SLICE_HEADER',
+                'UNMAPPED_SLICE_HEADER', // < only used in cram v1
                 'EXTERNAL_DATA',
                 'CORE_DATA',
             ][b];
@@ -65,7 +65,7 @@ const cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents
             const str = buffer.toString('utf8', stringStart, stringEnd);
             const tags = [];
             for (let i = 0; i < str.length; i += 3) {
-                tags.push(str.substr(i, 3));
+                tags.push(str.slice(i, i + 3));
             }
             return tags;
         }
@@ -121,8 +121,7 @@ const cramPreservationMap = new binary_parser_1.Parser()
 /* istanbul ignore next */
 function formatMap(data) {
     const map = {};
-    for (let i = 0; i < data.ents.length; i += 1) {
-        const { key, value } = data.ents[i];
+    for (const { key, value } of data.ents) {
         if (map[key]) {
             console.warn(`duplicate key ${key} in map`);
         }
@@ -206,7 +205,7 @@ const versionedParsers = {
         const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
         return { parser, maxLength: maxLengthFunc };
     },
-    cramEncoding(majorVersion) {
+    cramEncoding(_majorVersion) {
         const parser = new binary_parser_1.Parser()
             .namely('cramEncoding')
             .itf8('codecId')
@@ -214,9 +213,9 @@ const versionedParsers = {
             .choice('parameters', {
             tag: 'codecId',
             choices: {
-                0: new binary_parser_1.Parser(),
-                1: new binary_parser_1.Parser().itf8('blockContentId'),
-                2: new binary_parser_1.Parser().itf8('offset').itf8('M'),
+                0: new binary_parser_1.Parser(), // NULL
+                1: new binary_parser_1.Parser().itf8('blockContentId'), // EXTERNAL
+                2: new binary_parser_1.Parser().itf8('offset').itf8('M'), // GOLOMB,
                 // HUFFMAN_INT
                 3: binary_parser_1.Parser.start()
                     .itf8('numCodes')
@@ -228,9 +227,9 @@ const versionedParsers = {
                     .nest('valuesEncoding', { type: 'cramEncoding' }),
                 // BYTE_ARRAY_STOP is a little different for CRAM v1
                 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'),
+                6: new binary_parser_1.Parser().itf8('offset').itf8('length'), // BETA
+                7: new binary_parser_1.Parser().itf8('offset').itf8('K'), // SUBEXP
+                8: new binary_parser_1.Parser().itf8('offset').itf8('log2m'), // GOLOMB_RICE
                 9: new binary_parser_1.Parser().itf8('offset'), // GAMMA
             },
         });

package/dist/cramFile/sectionParsers.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -140,7 +140,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
         // map of operator name -> data series name
         const data1Schema = {
             B: ['character', 'BA'],
-            S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
+            S: ['string', majorVersion > 1 ? 'SC' : 'IN'], // IN if cram v1, SC otherwise
             X: ['number', 'BS'],
             D: ['number', 'DL'],
             I: ['string', 'IN'],
@@ -186,15 +186,11 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     // in javascript land.
     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 {
-        sequenceId = sliceHeader.parsedContent.refSeqId;
+        throw new Error('slice header not mapped');
     }
+    const sequenceId = majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2
+        ? decodeDataSeries('RI')
+        : sliceHeader.parsedContent.refSeqId;
     const readLength = decodeDataSeries('RL');
     // if APDelta, will calculate the true start in a second pass
     let alignmentStart = decodeDataSeries('AP');
@@ -257,8 +253,8 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     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 tagName = tagId.slice(0, 2);
+        const tagType = tagId.slice(2, 3);
         const tagCodec = compressionScheme.getCodecForTag(tagId);
         if (!tagCodec) {
             throw new errors_1.CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);

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

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -151,7 +151,7 @@ class CramSlice {
             const containerHeader = yield this.container.getHeader();
             const header = yield this.file.readBlock(containerHeader._endPosition + this.containerPosition);
             if (header === undefined) {
-                throw new Error();
+                throw new Error('block header undefined');
             }
             if (header.contentType === 'MAPPED_SLICE_HEADER') {
                 const content = (0, util_1.parseItem)(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
@@ -176,7 +176,7 @@ class CramSlice {
             for (let i = 0; i < blocks.length; i += 1) {
                 const block = yield this.file.readBlock(blockPosition);
                 if (block === undefined) {
-                    throw new Error();
+                    throw new Error('block undefined');
                 }
                 blocks[i] = block;
                 blockPosition = blocks[i]._endPosition;
@@ -216,16 +216,15 @@ class CramSlice {
             // read the slice header
             const sliceHeader = (yield this.getHeader()).parsedContent;
             if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader)) {
-                throw new Error();
+                throw new Error('slice header not mapped');
             }
             if (sliceHeader.refSeqId < 0) {
                 return undefined;
             }
             const compressionScheme = yield this.container.getCompressionScheme();
             if (compressionScheme === undefined) {
-                throw new Error();
+                throw new Error('compression scheme undefined');
             }
-            // console.log(JSON.stringify(sliceHeader, null, '  '))
             if (sliceHeader.refBaseBlockId >= 0) {
                 const refBlock = yield this.getBlockByContentId(sliceHeader.refBaseBlockId);
                 if (!refBlock) {
@@ -270,11 +269,11 @@ class CramSlice {
             const { majorVersion } = yield this.file.getDefinition();
             const compressionScheme = yield this.container.getCompressionScheme();
             if (compressionScheme === undefined) {
-                throw new Error();
+                throw new Error('compression scheme undefined');
             }
             const sliceHeader = yield this.getHeader();
             if (sliceHeader === undefined) {
-                throw new Error();
+                throw new Error('slice header undefined');
             }
             const blocksByContentId = yield this._getBlocksContentIdIndex();
             // check MD5 of reference if available
@@ -380,45 +379,48 @@ class CramSlice {
                         : undefined;
                     const compressionScheme = yield this.container.getCompressionScheme();
                     if (compressionScheme === undefined) {
-                        throw new Error();
+                        throw new Error('compression scheme undefined');
                     }
-                    const refRegions = {}; // seqId => { start, end, seq }
-                    // iterate over the records to find the spans of the reference sequences we need to fetch
-                    for (let i = 0; i < records.length; i += 1) {
-                        const seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                    const refRegions = {};
+                    // iterate over the records to find the spans of the reference
+                    // sequences we need to fetch
+                    for (const record of records) {
+                        const seqId = singleRefId !== undefined ? singleRefId : record.sequenceId;
                         let refRegion = refRegions[seqId];
                         if (!refRegion) {
                             refRegion = {
                                 id: seqId,
-                                start: records[i].alignmentStart,
+                                start: record.alignmentStart,
                                 end: -Infinity,
                                 seq: null,
                             };
                             refRegions[seqId] = refRegion;
                         }
-                        const end = records[i].alignmentStart +
-                            (records[i].lengthOnRef || records[i].readLength) -
+                        const end = record.alignmentStart +
+                            (record.lengthOnRef || record.readLength) -
                             1;
                         if (end > refRegion.end) {
                             refRegion.end = end;
                         }
-                        if (records[i].alignmentStart < refRegion.start) {
-                            refRegion.start = records[i].alignmentStart;
+                        if (record.alignmentStart < refRegion.start) {
+                            refRegion.start = record.alignmentStart;
                         }
                     }
                     // fetch the `seq` for all of the ref regions
                     yield Promise.all(Object.values(refRegions).map((refRegion) => __awaiter(this, void 0, void 0, function* () {
-                        if (refRegion.id !== -1 && refRegion.start <= refRegion.end) {
+                        if (refRegion.id !== -1 &&
+                            refRegion.start <= refRegion.end &&
+                            this.file.fetchReferenceSequenceCallback) {
                             refRegion.seq = yield this.file.fetchReferenceSequenceCallback(refRegion.id, refRegion.start, refRegion.end);
                         }
                     })));
                     // now decorate all the records with them
-                    for (let i = 0; i < records.length; i += 1) {
-                        const seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                    for (const record of records) {
+                        const seqId = singleRefId !== undefined ? singleRefId : record.sequenceId;
                         const refRegion = refRegions[seqId];
-                        if (refRegion && refRegion.seq) {
+                        if (refRegion === null || refRegion === void 0 ? void 0 : refRegion.seq) {
                             const seq = refRegion.seq;
-                            records[i].addReferenceSequence(Object.assign(Object.assign({}, refRegion), { seq }), compressionScheme);
+                            record.addReferenceSequence(Object.assign(Object.assign({}, refRegion), { seq }), compressionScheme);
                         }
                     }
                 }

package/dist/cramFile/slice/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cramFile/util.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 /// <reference types="node" />
 import { Parser } from '@gmod/binary-parser';
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;

package/dist/cramFile/util.js CHANGED Viewed

@@ -91,7 +91,7 @@ function tinyMemoize(_class, methodName) {
 }
 exports.tinyMemoize = tinyMemoize;
 function sequenceMD5(seq) {
-    return (0, md5_1.default)(seq.toUpperCase().replace(/[^\x21-\x7e]/g, ''));
+    return (0, md5_1.default)(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
 exports.sequenceMD5 = sequenceMD5;
 //# sourceMappingURL=util.js.map

package/dist/cramFile/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/index.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-import CramFile, { CramRecord } from './cramFile';
-import IndexedCramFile from './indexedCramFile';
-import CraiIndex from './craiIndex';
-export { CramFile, IndexedCramFile, CraiIndex, CramRecord };
+export { default as CramFile, CramRecord } from './cramFile';
+export { default as CraiIndex } from './craiIndex';
+export { default as IndexedCramFile } from './indexedCramFile';

package/dist/index.js CHANGED Viewed

@@ -1,37 +1,14 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CramRecord = exports.CraiIndex = exports.IndexedCramFile = exports.CramFile = void 0;
-const cramFile_1 = __importStar(require("./cramFile"));
-exports.CramFile = cramFile_1.default;
+exports.IndexedCramFile = exports.CraiIndex = exports.CramRecord = exports.CramFile = void 0;
+var cramFile_1 = require("./cramFile");
+Object.defineProperty(exports, "CramFile", { enumerable: true, get: function () { return __importDefault(cramFile_1).default; } });
 Object.defineProperty(exports, "CramRecord", { enumerable: true, get: function () { return cramFile_1.CramRecord; } });
-const indexedCramFile_1 = __importDefault(require("./indexedCramFile"));
-exports.IndexedCramFile = indexedCramFile_1.default;
-const craiIndex_1 = __importDefault(require("./craiIndex"));
-exports.CraiIndex = craiIndex_1.default;
+var craiIndex_1 = require("./craiIndex");
+Object.defineProperty(exports, "CraiIndex", { enumerable: true, get: function () { return __importDefault(craiIndex_1).default; } });
+var indexedCramFile_1 = require("./indexedCramFile");
+Object.defineProperty(exports, "IndexedCramFile", { enumerable: true, get: function () { return __importDefault(indexedCramFile_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~AAAA,~~uDAAiD~~;~~AAIxC~~,~~mBAJF~~,~~kBAAQ~~,~~CAIE~~;~~AAA8B~~,~~2FAJ5B~~,~~qBAAU~~,~~OAI4B~~;~~AAHzD~~,~~wEAA+C~~;~~AAG5B~~,~~0BAHZ~~,~~yBAAe~~,~~CAGY~~;~~AAFlC~~,~~4DAAmC~~;~~AAEC~~,~~oBAF7B~~,~~mBAAS~~,~~CAE6B~~"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,uCAA4D;AAAnD,qHAAA,OAAO,OAAY;AAAE,sGAAA,UAAU,OAAA;AACxC,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,qDAA8D;AAArD,mIAAA,OAAO,OAAmB"}

package/dist/indexedCramFile.d.ts CHANGED Viewed

@@ -3,15 +3,15 @@ import CramRecord from './cramFile/record';
 import { SeqFetch } from './cramFile/file';
 import { Filehandle } from './cramFile/filehandle';
 import { Slice } from './craiIndex';
-export type CramFileSource = {
+export interface CramFileSource {
     cramFilehandle?: Filehandle;
     cramUrl?: string;
     cramPath?: string;
-};
-export type CramIndexLike = {
+}
+export interface CramIndexLike {
     getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;
     hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;
-};
+}
 export default class IndexedCramFile {
     cram: CramFile;
     index: CramIndexLike;
@@ -33,8 +33,8 @@ export default class IndexedCramFile {
         cram: CramFile;
     } | ({
         cram?: undefined;
-        seqFetch: SeqFetch;
-        checkSequenceMD5: boolean;
+        seqFetch?: SeqFetch;
+        checkSequenceMD5?: boolean;
         cacheSize?: number;
     } & CramFileSource)));
     /**