npm - @gmod/cram - Versions diffs - 1.7.4 → 2.0.1 - Mend

@gmod/cram 1.7.4 → 2.0.1

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 (104) hide show

package/CHANGELOG.md +9 -2
package/README.md +343 -24
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cram-bundle.js.LICENSE.txt +6 -0
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.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.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.map +1 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +10 -3
package/dist/cramFile/file.js +56 -50
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.d.ts +1 -0
package/dist/cramFile/sectionParsers.js +7 -7
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +1 -1
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +1 -0
package/dist/cramFile/util.js.map +1 -1
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.js.map +1 -1
package/dist/rans/constants.d.ts +4 -3
package/dist/rans/constants.js.map +1 -1
package/dist/rans/d04.js +1 -0
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js +1 -0
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.d.ts +16 -19
package/dist/rans/decoding.js +1 -0
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.d.ts +2 -2
package/dist/rans/frequencies.js +1 -0
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js +1 -0
package/dist/rans/index.js.map +1 -1
package/dist/sam.d.ts +5 -6
package/dist/sam.js +23 -7
package/dist/sam.js.map +1 -1
package/dist/typescript.js.map +1 -1
package/dist/unzip.d.ts +1 -0
package/esm/craiIndex.js.map +1 -1
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.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.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.map +1 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +10 -3
package/esm/cramFile/file.js +17 -13
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.d.ts +1 -0
package/esm/cramFile/sectionParsers.js +7 -7
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +1 -1
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +1 -0
package/esm/cramFile/util.js.map +1 -1
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.js.map +1 -1
package/esm/rans/constants.d.ts +4 -3
package/esm/rans/constants.js.map +1 -1
package/esm/rans/d04.js +1 -0
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js +1 -0
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.d.ts +16 -19
package/esm/rans/decoding.js +1 -0
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.d.ts +2 -2
package/esm/rans/frequencies.js +1 -0
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js +1 -0
package/esm/rans/index.js.map +1 -1
package/esm/sam.d.ts +5 -6
package/esm/sam.js +23 -7
package/esm/sam.js.map +1 -1
package/esm/typescript.js.map +1 -1
package/esm/unzip.d.ts +1 -0
package/package.json +11 -10
package/src/cramFile/container/index.ts +4 -1
package/src/cramFile/file.ts +23 -19
package/src/rans/{d04.js → d04.ts} +1 -0
package/src/rans/{d14.js → d14.ts} +1 -0
package/src/rans/{decoding.js → decoding.ts} +1 -0
package/src/rans/{frequencies.js → frequencies.ts} +1 -0
package/src/rans/{index.js → index.ts} +1 -0
package/src/sam.ts +30 -14
/package/src/rans/{constants.js → constants.ts} +0 -0

package/dist/cram-bundle.js.LICENSE.txt CHANGED Viewed

@@ -1,3 +1,9 @@
+/*!
+ * Based on xzwasm (c) Steve Sanderson. License: MIT - https://github.com/SteveSanderson/xzwasm
+ * Contains xz-embedded by Lasse Collin and Igor Pavlov. License: Public domain - https://tukaani.org/xz/embedded.html
+ * and walloc (c) 2020 Igalia, S.L. License: MIT - https://github.com/wingo/walloc
+ */
 /*!
  * Determine if an object is a Buffer
  *

package/dist/cramFile/codecs/beta.js.map CHANGED Viewed

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

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

@@ -1,8 +1,9 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 /// <reference types="node" />
 import QuickLRU from 'quick-lru';
+import { Parser } from '@gmod/binary-parser';
 import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
-import { Parser } from '@gmod/binary-parser';
 import CramRecord from './record';
 import { Filehandle } from './filehandle';
 export type CramFileSource = {
@@ -40,7 +41,13 @@ export default class CramFile {
     }>;
     stat(): Promise<import("generic-filehandle").Stats>;
     getDefinition(): Promise<any>;
-    getSamHeader(): Promise<import("../sam").HeaderDataItem[]>;
+    getSamHeader(): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string | undefined;
+        }[];
+    }[]>;
     getHeaderText(): Promise<string | undefined>;
     getSectionParsers(): Promise<{
         cramFileDefinition: {
@@ -108,6 +115,6 @@ export default class CramFile {
         parser: Parser<T>;
         maxLength: number;
     }, position: number, size?: number, preReadBuffer?: undefined): Promise<import("./util").ParsedItem<T> | undefined>;
-    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): void;
+    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): Promise<void>;
     readBlock(position: number): Promise<CramFileBlock | undefined>;
 }

package/dist/cramFile/file.js CHANGED Viewed

@@ -15,16 +15,25 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const unzip_1 = require("../unzip");
 const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
+const htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
 // @ts-expect-error
 const bzip2_1 = __importDefault(require("bzip2"));
+const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
 const rans_1 = __importDefault(require("../rans"));
 const sectionParsers_1 = require("./sectionParsers");
-const htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
 const container_1 = __importDefault(require("./container"));
 const io_1 = require("../io");
 const util_1 = require("./util");
 const sam_1 = require("../sam");
+function bufferToStream(buf) {
+    return new ReadableStream({
+        start(controller) {
+            controller.enqueue(buf);
+            controller.close();
+        },
+    });
+}
 //source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
     const uInt32 = new Uint32Array([0x11223344]);
@@ -60,16 +69,6 @@ class CramFile {
             throw new Error('Detected big-endian machine, may be unable to run');
         }
     }
-    // toString() {
-    //   if (this.file.filename) {
-    //     return this.file.filename
-    //   }
-    //   if (this.file.url) {
-    //     return this.file.url
-    //   }
-    //
-    //   return '(cram file)'
-    // }
     // can just read this object like a filehandle
     read(buffer, offset, length, position) {
         return this.file.read(buffer, offset, length, position);
@@ -253,44 +252,51 @@ class CramFile {
         });
     }
     _uncompress(compressionMethod, inputBuffer, outputBuffer) {
-        if (compressionMethod === 'gzip') {
-            const result = (0, unzip_1.unzip)(inputBuffer);
-            result.copy(outputBuffer);
-        }
-        else if (compressionMethod === 'bzip2') {
-            const bits = bzip2_1.default.array(inputBuffer);
-            let size = bzip2_1.default.header(bits);
-            let j = 0;
-            let chunk;
-            do {
-                chunk = bzip2_1.default.decompress(bits, size);
-                if (chunk != -1) {
-                    Buffer.from(chunk).copy(outputBuffer, j);
-                    j += chunk.length;
-                    size -= chunk.length;
-                }
-            } while (chunk != -1);
-        }
-        else if (compressionMethod === 'rans') {
-            (0, rans_1.default)(inputBuffer, outputBuffer);
-            //htscodecs r4x8 is slower, but compatible.
-            //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
-        }
-        else if (compressionMethod === 'rans4x16') {
-            htscodecs_1.default.r4x16_uncompress(inputBuffer, outputBuffer);
-        }
-        else if (compressionMethod === 'arith') {
-            htscodecs_1.default.arith_uncompress(inputBuffer, outputBuffer);
-        }
-        else if (compressionMethod === 'fqzcomp') {
-            htscodecs_1.default.fqzcomp_uncompress(inputBuffer, outputBuffer);
-        }
-        else if (compressionMethod === 'tok3') {
-            htscodecs_1.default.tok3_uncompress(inputBuffer, outputBuffer);
-        }
-        else {
-            throw new errors_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
-        }
+        return __awaiter(this, void 0, void 0, function* () {
+            if (compressionMethod === 'gzip') {
+                const result = (0, unzip_1.unzip)(inputBuffer);
+                result.copy(outputBuffer);
+            }
+            else if (compressionMethod === 'bzip2') {
+                const bits = bzip2_1.default.array(inputBuffer);
+                let size = bzip2_1.default.header(bits);
+                let j = 0;
+                let chunk;
+                do {
+                    chunk = bzip2_1.default.decompress(bits, size);
+                    if (chunk != -1) {
+                        Buffer.from(chunk).copy(outputBuffer, j);
+                        j += chunk.length;
+                        size -= chunk.length;
+                    }
+                } while (chunk != -1);
+            }
+            else if (compressionMethod === 'lzma') {
+                const decompressedResponse = new Response(new xz_decompress_1.XzReadableStream(bufferToStream(inputBuffer)));
+                const ret = Buffer.from(yield decompressedResponse.arrayBuffer());
+                ret.copy(outputBuffer);
+            }
+            else if (compressionMethod === 'rans') {
+                (0, rans_1.default)(inputBuffer, outputBuffer);
+                //htscodecs r4x8 is slower, but compatible.
+                //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
+            }
+            else if (compressionMethod === 'rans4x16') {
+                htscodecs_1.default.r4x16_uncompress(inputBuffer, outputBuffer);
+            }
+            else if (compressionMethod === 'arith') {
+                htscodecs_1.default.arith_uncompress(inputBuffer, outputBuffer);
+            }
+            else if (compressionMethod === 'fqzcomp') {
+                htscodecs_1.default.fqzcomp_uncompress(inputBuffer, outputBuffer);
+            }
+            else if (compressionMethod === 'tok3') {
+                htscodecs_1.default.tok3_uncompress(inputBuffer, outputBuffer);
+            }
+            else {
+                throw new errors_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
+            }
+        });
     }
     readBlock(position) {
         return __awaiter(this, void 0, void 0, function* () {
@@ -306,7 +312,7 @@ class CramFile {
             if (blockHeader.compressionMethod !== 'raw') {
                 const compressedData = Buffer.allocUnsafe(blockHeader.compressedSize);
                 yield this.read(compressedData, 0, blockHeader.compressedSize, blockContentPosition);
-                this._uncompress(blockHeader.compressionMethod, compressedData, uncompressedData);
+                yield this._uncompress(blockHeader.compressionMethod, compressedData, uncompressedData);
             }
             else {
                 yield this.read(uncompressedData, 0, blockHeader.uncompressedSize, blockContentPosition);

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

	@@ -1 +1 @@
1	- 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package/dist/cramFile/record.js.map CHANGED Viewed

	@@ -1 +1 @@
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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';

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];
@@ -214,9 +214,9 @@ 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 +228,9 @@ 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 @@
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'],

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

	@@ -1 +1 @@
1	- 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