@gmod/cram 4.0.1 → 4.0.4

package/dist/cramFile/file.js

@@ -1,4 +1,37 @@
 "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 () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -8,14 +41,15 @@ const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
-const htscodecs_1 = __importDefault(require("../htscodecs"));
+const htscodecs = __importStar(require("../htscodecs"));
 const io_1 = require("../io");
 const rans_1 = __importDefault(require("../rans"));
 const sam_1 = require("../sam");
 const unzip_1 = require("../unzip");
+const util_1 = require("../util");
 const container_1 = __importDefault(require("./container"));
 const sectionParsers_1 = require("./sectionParsers");
-const util_1 = require("./util");
+const util_2 = require("./util");
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -199,7 +233,7 @@ class CramFile {
             return undefined;
         }
         const buffer = await this.file.read(cramBlockHeader.maxLength, position);
-        return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
+        return (0, util_2.parseItem)(buffer, cramBlockHeader.parser, 0, position);
     }
     async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
         let buffer;
@@ -213,7 +247,7 @@ class CramFile {
             }
             buffer = await this.file.read(size, position);
         }
-        const data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
+        const data = (0, util_2.parseItem)(buffer, section.parser, 0, position);
         if (data._size !== size) {
             throw new errors_1.CramMalformedError(`section read error: requested size ${size} does not equal parsed size ${data._size}`);
         }
@@ -249,16 +283,16 @@ class CramFile {
             // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
         }
         else if (compressionMethod === 'rans4x16') {
-            return htscodecs_1.default.r4x16_uncompress(inputBuffer);
+            return htscodecs.r4x16_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'arith') {
-            return htscodecs_1.default.arith_uncompress(inputBuffer);
+            return htscodecs.arith_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'fqzcomp') {
-            return htscodecs_1.default.fqzcomp_uncompress(inputBuffer);
+            return htscodecs.fqzcomp_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'tok3') {
-            return htscodecs_1.default.tok3_uncompress(inputBuffer);
+            return htscodecs.tok3_uncompress(inputBuffer);
         }
         else {
             throw new errors_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
@@ -307,6 +341,6 @@ class CramFile {
 }
 exports.default = CramFile;
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
-    (0, util_1.tinyMemoize)(CramFile, method);
+    (0, util_2.tinyMemoize)(CramFile, method);
 });
 //# sourceMappingURL=file.js.map

package/dist/cramFile/file.js.map

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

@@ -118,15 +118,15 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
         if (type === 'character') {
             return String.fromCharCode(data);
         }
-        if (type === 'string') {
+        else if (type === 'string') {
             let r = '';
             for (let i = 0; i < data.byteLength; i++) {
                 r += String.fromCharCode(data[i]);
             }
             return r;
         }
-        if (type === 'numArray') {
-            return data.toArray();
+        else if (type === 'numArray') {
+            return Array.from(data);
         }
         // else if (type === 'number') {
         //   return data[0]

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

@@ -1 +1 @@
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package/dist/cramFile/slice/index.d.ts

@@ -39,7 +39,7 @@ export default class CramSlice {
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
     getBlockByContentId(id: number): Promise<CramFileBlock | undefined>;
     getReferenceRegion(): Promise<{
-        seq: any;
+        seq: string;
         start: number;
         end: number;
         span: number;

package/dist/cramFile/slice/index.js

@@ -196,6 +196,7 @@ class CramSlice {
     }
     async getReferenceRegion() {
         // read the slice header
+        const decoder = new TextDecoder('utf8');
         const sliceHeader = (await this.getHeader()).parsedContent;
         if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader)) {
             throw new Error('slice header not mapped');
@@ -218,7 +219,8 @@ class CramSlice {
             // }
             // TODO verify
             return {
-                seq: refBlock.data.toString('utf8'),
+                // @ts-expect-error
+                seq: decoder.decode(refBlock.data),
                 start: sliceHeader.refSeqStart,
                 end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
                 span: sliceHeader.refSeqSpan,

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

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

@@ -10,5 +10,3 @@ export declare function parseItem<T>(buffer: Uint8Array, parser: (buffer: Uint8A
 };
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;
-export declare function sum(array: Uint8Array[]): number;
-export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;

package/dist/cramFile/util.js

@@ -9,9 +9,7 @@ exports.parseLtf8 = parseLtf8;
 exports.parseItem = parseItem;
 exports.tinyMemoize = tinyMemoize;
 exports.sequenceMD5 = sequenceMD5;
-exports.sum = sum;
-exports.concatUint8Array = concatUint8Array;
-const long_1 = __importDefault(require("long"));
+const longfn_1 = require("longfn");
 const md5_1 = __importDefault(require("md5"));
 const getBits_1 = require("./codecs/getBits");
 function itf8Size(v) {
@@ -134,21 +132,11 @@ function parseLtf8(buffer, initialOffset) {
         offset += 7;
     }
     else if (countFlags < 0xff) {
-        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 8));
-        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
-            n.lessThan(Number.MIN_SAFE_INTEGER)) {
-            throw new Error('integer overflow');
-        }
-        n = n.toNumber();
+        n = (0, longfn_1.toNumber)((0, longfn_1.fromBytesBE)(buffer.slice(offset + 1, offset + 8), false));
         offset += 8;
     }
     else {
-        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 9));
-        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
-            n.lessThan(Number.MIN_SAFE_INTEGER)) {
-            throw new Error('integer overflow');
-        }
-        n = n.toNumber();
+        n = (0, longfn_1.toNumber)((0, longfn_1.fromBytesBE)(buffer.subarray(offset + 1, offset + 9), false));
         offset += 9;
     }
     return [n, offset - initialOffset];
@@ -182,20 +170,4 @@ function tinyMemoize(_class, methodName) {
 function sequenceMD5(seq) {
     return (0, md5_1.default)(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
-function sum(array) {
-    let sum = 0;
-    for (const entry of array) {
-        sum += entry.length;
-    }
-    return sum;
-}
-function concatUint8Array(args) {
-    const mergedArray = new Uint8Array(sum(args));
-    let offset = 0;
-    for (const entry of args) {
-        mergedArray.set(entry, offset);
-        offset += entry.length;
-    }
-    return mergedArray;
-}
 //# sourceMappingURL=util.js.map

package/dist/cramFile/util.js.map

@@ -1 +1 @@
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package/dist/htscodecs/arith_gen.d.ts

@@ -1,18 +1,16 @@
-export = RangeCoderGen;
-declare class RangeCoderGen {
-    decode(src: any): Uint8Array<any>;
-    stream: IOStream | undefined;
-    decodeStream(stream: any, n_out?: number): Uint8Array<any>;
+import IOStream from './iostream';
+export default class RangeCoderGen {
+    stream: IOStream;
+    decode(src: Uint8Array): Uint8Array<any>;
+    decodeStream(stream: IOStream, n_out?: number): Uint8Array<any>;
     decode0(stream: any, n_out: any): Uint8Array<any>;
     decode1(stream: any, n_out: any): Uint8Array<any>;
     decodeExt(stream: any, n_out: any): Uint8Array<ArrayBuffer>;
     decodeRLE0(stream: any, n_out: any): Uint8Array<any>;
     decodeRLE1(stream: any, n_out: any): Uint8Array<any>;
     decodePackMeta(stream: any): any[];
-    nsym: any;
     decodePack(data: any, M: any, len: any): any;
     packMeta(src: any): (number | any[] | IOStream)[];
     decodeStripe(stream: any, len: any): Uint8Array<any>;
     decodeCat(stream: any, len: any): Uint8Array<any>;
 }
-import IOStream = require("./iostream");