npm - @gmod/cram - Versions diffs - 2.0.1 → 2.0.2 - Mend

@gmod/cram 2.0.1 → 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 (109) 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/external.js +1 -0
package/dist/cramFile/codecs/external.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/container/compressionScheme.js +1 -1
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/encoding.d.ts +20 -20
package/dist/cramFile/file.d.ts +6 -6
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 +8 -8
package/dist/cramFile/sectionParsers.js +3 -4
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +6 -10
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.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/sam.js +10 -13
package/dist/sam.js.map +1 -1
package/dist/unzip.d.ts +1 -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/external.js +1 -0
package/esm/cramFile/codecs/external.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/container/compressionScheme.js +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/encoding.d.ts +20 -20
package/esm/cramFile/file.d.ts +6 -6
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 +8 -8
package/esm/cramFile/sectionParsers.js +3 -4
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +6 -10
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.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/sam.js +10 -13
package/esm/sam.js.map +1 -1
package/esm/unzip.d.ts +1 -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 +12 -14
package/src/typings/binary-parser.d.ts +1 -1
package/src/unzip.ts +1 -2

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

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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.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 @@
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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)));
     /**

package/dist/indexedCramFile.js CHANGED Viewed

@@ -26,12 +26,10 @@ class IndexedCramFile {
      * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
      */
     constructor(args) {
+        var _a;
         // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
-        if (args.cram) {
-            this.cram = args.cram;
-        }
-        else {
-            this.cram = new cramFile_1.default({
+        this.cram =
+            (_a = args.cram) !== null && _a !== void 0 ? _a : new cramFile_1.default({
                 url: args.cramUrl,
                 path: args.cramPath,
                 filehandle: args.cramFilehandle,
@@ -39,7 +37,6 @@ class IndexedCramFile {
                 checkSequenceMD5: args.checkSequenceMD5,
                 cacheSize: args.cacheSize,
             });
-        }
         if (!(this.cram instanceof cramFile_1.default)) {
             throw new Error('invalid arguments: no cramfile');
         }
@@ -82,12 +79,12 @@ class IndexedCramFile {
             if (opts.viewAsPairs) {
                 const readNames = {};
                 const readIds = {};
-                for (let i = 0; i < ret.length; i += 1) {
-                    const name = ret[i].readName;
+                for (const read of ret) {
+                    const name = read.readName;
                     if (name === undefined) {
-                        throw new Error();
+                        throw new Error('readName undefined');
                     }
-                    const id = ret[i].uniqueId;
+                    const id = read.uniqueId;
                     if (!readNames[name]) {
                         readNames[name] = 0;
                     }
@@ -101,11 +98,10 @@ class IndexedCramFile {
                     }
                 });
                 const matePromises = [];
-                for (let i = 0; i < ret.length; i += 1) {
-                    const cramRecord = ret[i];
+                for (const cramRecord of ret) {
                     const name = cramRecord.readName;
                     if (name === undefined) {
-                        throw new Error();
+                        throw new Error('readName undefined');
                     }
                     if (unmatedPairs[name] &&
                         cramRecord.mate &&
@@ -118,8 +114,8 @@ class IndexedCramFile {
                 }
                 const mateBlocks = yield Promise.all(matePromises);
                 let mateChunks = [];
-                for (let i = 0; i < mateBlocks.length; i += 1) {
-                    mateChunks.push(...mateBlocks[i]);
+                for (const block of mateBlocks) {
+                    mateChunks.push(...block);
                 }
                 // filter out duplicates
                 mateChunks = mateChunks
@@ -142,10 +138,9 @@ class IndexedCramFile {
                     mateRecordPromises.push(recordPromise);
                     const featPromise = recordPromise.then(feats => {
                         const mateRecs = [];
-                        for (let i = 0; i < feats.length; i += 1) {
-                            const feature = feats[i];
+                        for (const feature of feats) {
                             if (feature.readName === undefined) {
-                                throw new Error();
+                                throw new Error('readName undefined');
                             }
                             if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
                                 mateRecs.push(feature);

package/dist/indexedCramFile.js.map CHANGED Viewed

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

@@ -2,4 +2,5 @@ import { Filehandle } from '../cramFile/filehandle';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
 declare function fromUrl(source: string): LocalFile | RemoteFile;
 declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
-export { LocalFile, RemoteFile, fromUrl, open };
+export { fromUrl, open };
+export { LocalFile, RemoteFile } from 'generic-filehandle';

package/dist/io/index.js CHANGED Viewed

@@ -3,12 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.open = exports.fromUrl = exports.RemoteFile = exports.LocalFile = void 0;
+exports.RemoteFile = exports.LocalFile = exports.open = exports.fromUrl = void 0;
 const url_1 = __importDefault(require("url"));
 const typescript_1 = require("../typescript");
 const generic_filehandle_1 = require("generic-filehandle");
-Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_1.LocalFile; } });
-Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_1.RemoteFile; } });
 function fromUrl(source) {
     const { protocol, pathname } = url_1.default.parse(source);
     if (protocol === 'file:') {
@@ -30,4 +28,7 @@ function open(maybeUrl, maybePath, maybeFilehandle) {
     throw new Error('no url, path, or filehandle provided, cannot open');
 }
 exports.open = open;
+var generic_filehandle_2 = require("generic-filehandle");
+Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_2.LocalFile; } });
+Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_2.RemoteFile; } });
 //# sourceMappingURL=index.js.map

package/dist/io/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AACrB,8CAAgD;AAEhD,2DAA0D;~~AA2BjD~~,~~0FA3BA,8BAAS,OA2BA;AAAE,2FA3BA,+BAAU,OA2BA;AAzB9B,~~SAAS,OAAO,CAAC,MAAc;IAC7B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,aAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE,CAAC;QACzB,OAAO,IAAI,8BAAS,CAAC,QAAQ,CAAC,IAAA,6BAAgB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,+BAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;~~AAmB+B~~,0BAAO;~~AAjBvC~~,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAA4B;IAE5B,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC1B,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,8BAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;~~AAEwC~~,oBAAI"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AACrB,8CAAgD;AAEhD,2DAA0D;AAE1D,SAAS,OAAO,CAAC,MAAc;IAC7B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,aAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE,CAAC;QACzB,OAAO,IAAI,8BAAS,CAAC,QAAQ,CAAC,IAAA,6BAAgB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,+BAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAmBQ,0BAAO;AAjBhB,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAA4B;IAE5B,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC1B,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,8BAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAEiB,oBAAI;AAEtB,yDAA0D;AAAjD,+GAAA,SAAS,OAAA;AAAE,gHAAA,UAAU,OAAA"}

package/dist/sam.js CHANGED Viewed

@@ -11,21 +11,18 @@ function parseHeaderText(text) {
                 tag: tag.slice(1),
                 data: fields.map(f => {
                     const r = f.indexOf(':');
-                    if (r !== -1) {
-                        return {
+                    return r !== -1
+                        ? {
                             tag: f.slice(0, r),
                             value: f.slice(r + 1),
-                        };
-                    }
-                    else {
-                        // @CO lines are not comma separated.
-                        // See "samtools view -H c2\#pad.3.0.cram"
-                        // so, just store value tag itself
-                        return {
-                            tag: f,
-                            value: undefined,
-                        };
-                    }
+                        }
+                        : // @CO lines are not comma separated.
+                            // See "samtools view -H c2\#pad.3.0.cram"
+                            // so, just store value tag itself
+                            {
+                                tag: f,
+                                value: undefined,
+                            };
                 }),
             });
         }

package/dist/sam.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,~~IAAI~~,CAAC,KAAK,CAAC,CAAC,~~EAAE~~,CAAC;~~wBACb~~,~~OAAO;4BACL,~~GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB~~,CAAA~~;~~oBACH~~,CAAC~~;yBAAM~~,CAAC~~;wBACN~~,qCAAqC;~~wBACrC~~,0CAA0C;~~wBAC1C~~,kCAAkC;~~wBAClC,OAAO~~;~~4BACL~~,GAAG,EAAE,CAAC;~~4BACN~~,KAAK,EAAE,SAAS;~~yBACjB~~,CAAA;~~oBACH~~,CAAC~~;gBACH~~,CAAC~~,CAAC~~;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;~~AAnCD~~,~~0CAmCC~~"}
1	+ {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC;4BACE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB;wBACH,CAAC,CAAC,qCAAqC;4BACrC,0CAA0C;4BAC1C,kCAAkC;4BAClC;gCACE,GAAG,EAAE,CAAC;gCACN,KAAK,EAAE,SAAS;6BACjB,CAAA;gBACP,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAjCD,0CAiCC"}

package/dist/unzip.d.ts CHANGED Viewed

@@ -1,3 +1,2 @@
 /// <reference types="node" />
-import { gunzipSync } from 'zlib';
-export { gunzipSync as unzip };
+export { gunzipSync as unzip } from 'zlib';

package/dist/unzip.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = void 0;
-const zlib_1 = require("zlib");
+var zlib_1 = require("zlib");
 Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.gunzipSync; } });
 //# sourceMappingURL=unzip.js.map

package/dist/unzip.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA~~,+BAAiC~~;~~AACV~~,~~sFADd~~,~~iBAAU~~,~~OACS~~"}
1	+ {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAA0C;AAAjC,6FAAA,UAAU,OAAS"}

package/esm/craiIndex.d.ts CHANGED Viewed

@@ -1,11 +1,11 @@
 import { CramFileSource } from './cramFile/file';
-export type Slice = {
+export interface Slice {
     start: number;
     span: number;
     containerStart: number;
     sliceStart: number;
     sliceBytes: number;
-};
+}
 type ParsedIndex = Record<string, Slice[]>;
 export default class CraiIndex {
     private _parseCache;