npm - @gmod/cram - Versions diffs - 3.0.3 → 3.0.5 - Mend

@gmod/cram 3.0.3 → 3.0.5

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 (106) hide show

package/dist/craiIndex.d.ts +3 -5
package/dist/craiIndex.js +28 -30
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/byteArrayLength.js +3 -6
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.d.ts +0 -1
package/dist/cramFile/codecs/byteArrayStop.js +0 -6
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.js +0 -1
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.js +1 -2
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/container/compressionScheme.d.ts +1 -1
package/dist/cramFile/container/compressionScheme.js +12 -4
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.js +3 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +1 -1
package/dist/cramFile/file.js +11 -12
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js +1 -7
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +6 -11
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.d.ts +3 -2
package/dist/cramFile/slice/index.js +10 -16
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/indexedCramFile.js +0 -3
package/dist/indexedCramFile.js.map +1 -1
package/dist/rans/d04.js +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.js +1 -1
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.js +1 -1
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js +1 -1
package/dist/rans/index.js.map +1 -1
package/esm/craiIndex.d.ts +3 -5
package/esm/craiIndex.js +63 -64
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js +3 -6
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.d.ts +0 -1
package/esm/cramFile/codecs/byteArrayStop.js +0 -6
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.js +0 -1
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.js +1 -2
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/container/compressionScheme.d.ts +1 -1
package/esm/cramFile/container/compressionScheme.js +12 -4
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.js +3 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +1 -1
package/esm/cramFile/file.js +10 -11
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js +1 -7
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +6 -8
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.d.ts +3 -2
package/esm/cramFile/slice/index.js +10 -16
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.js.map +1 -1
package/esm/indexedCramFile.js +0 -3
package/esm/indexedCramFile.js.map +1 -1
package/esm/rans/d04.js +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js +1 -1
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.js +1 -1
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.js +1 -1
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js +1 -1
package/esm/rans/index.js.map +1 -1
package/package.json +10 -10
package/src/craiIndex.ts +82 -81
package/src/cramFile/codecs/byteArrayLength.ts +3 -8
package/src/cramFile/codecs/byteArrayStop.ts +0 -12
package/src/cramFile/codecs/external.ts +1 -2
package/src/cramFile/codecs/getBits.ts +1 -1
package/src/cramFile/codecs/huffman.ts +11 -12
package/src/cramFile/container/compressionScheme.ts +38 -31
package/src/cramFile/container/index.ts +3 -1
package/src/cramFile/file.ts +10 -11
package/src/cramFile/record.ts +3 -10
package/src/cramFile/sectionParsers.ts +4 -4
package/src/cramFile/slice/decodeRecord.ts +22 -32
package/src/cramFile/slice/index.ts +16 -25
package/src/cramFile/util.ts +36 -35
package/src/indexedCramFile.ts +1 -4
package/src/rans/d04.ts +1 -1
package/src/rans/d14.ts +1 -1
package/src/rans/decoding.ts +1 -1
package/src/rans/frequencies.ts +1 -1
package/src/rans/index.ts +1 -1

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

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package/dist/cramFile/slice/index.d.ts CHANGED Viewed

@@ -8,8 +8,9 @@ export type SliceHeader = CramFileBlock & {
 export default class CramSlice {
     container: CramContainer;
     containerPosition: number;
+    sliceSize: number;
     private file;
-    constructor(container: CramContainer, containerPosition: number, _unused: number);
+    constructor(container: CramContainer, containerPosition: number, sliceSize: number);
     getHeader(): Promise<{
         parsedContent: {
             recordCounter: number;
@@ -36,7 +37,7 @@ export default class CramSlice {
     getBlocks(): Promise<CramFileBlock[]>;
     getCoreDataBlock(): Promise<CramFileBlock>;
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
-    getBlockByContentId(id: number): Promise<CramFileBlock>;
+    getBlockByContentId(id: number): Promise<CramFileBlock | undefined>;
     getReferenceRegion(): Promise<{
         seq: any;
         start: number;

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

@@ -69,14 +69,12 @@ function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
     mateRecord.templateLength = lengthEstimate;
 }
 /**
- * @private establishes a mate-pair relationship between two records in the same slice.
- * CRAM compresses mate-pair relationships between records in the same slice down into
- * just one record having the index in the slice of its mate
+ * @private establishes a mate-pair relationship between two records in the
+ * same slice. CRAM compresses mate-pair relationships between records in the
+ * same slice down into just one record having the index in the slice of its
+ * mate
  */
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
-    if (!mateRecord) {
-        throw new errors_1.CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
-    }
     const complicatedMultiSegment = !!(mateRecord.mate ||
         (mateRecord.mateRecordNumber !== undefined &&
             mateRecord.mateRecordNumber !== currentRecordNumber));
@@ -138,9 +136,10 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     thisRecord.mateRecordNumber = undefined;
 }
 class CramSlice {
-    constructor(container, containerPosition, _unused) {
+    constructor(container, containerPosition, sliceSize) {
         this.container = container;
         this.containerPosition = containerPosition;
+        this.sliceSize = sliceSize;
         this.file = container.file;
     }
     // memoize
@@ -192,7 +191,6 @@ class CramSlice {
     getCoreDataBlock() {
         return __awaiter(this, void 0, void 0, function* () {
             const blocks = yield this.getBlocks();
-            // the core data block is always the first block in the slice
             return blocks[0];
         });
     }
@@ -277,9 +275,6 @@ class CramSlice {
                 throw new Error('compression scheme undefined');
             }
             const sliceHeader = yield this.getHeader();
-            if (sliceHeader === undefined) {
-                throw new Error('slice header undefined');
-            }
             const blocksByContentId = yield this._getBlocksContentIdIndex();
             // check MD5 of reference if available
             if (majorVersion > 1 &&
@@ -328,7 +323,7 @@ class CramSlice {
                 const decoded = codec.decode(this, coreDataBlock, blocksByContentId, cursors);
                 return decoded;
             };
-            let records = new Array(sliceHeader.parsedContent.numRecords);
+            const records = new Array(sliceHeader.parsedContent.numRecords);
             for (let i = 0; i < records.length; i += 1) {
                 try {
                     const init = (0, decodeRecord_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
@@ -340,7 +335,6 @@ class CramSlice {
                 catch (e) {
                     if (e instanceof getBits_1.CramBufferOverrunError) {
                         console.warn('read attempted beyond end of buffer, file seems truncated.');
-                        records = records.filter(r => !!r);
                         break;
                     }
                     else {
@@ -434,7 +428,7 @@ class CramSlice {
 }
 exports.default = CramSlice;
 // memoize several methods in the class for performance
-'getHeader getBlocks _getBlocksContentIdIndex'
-    .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(CramSlice, method));
+'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
+    (0, util_1.tinyMemoize)(CramSlice, method);
+});
 //# sourceMappingURL=index.js.map

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

	@@ -1 +1 @@
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package/dist/indexedCramFile.js CHANGED Viewed

@@ -40,9 +40,6 @@ class IndexedCramFile {
             throw new Error('invalid arguments: no cramfile');
         }
         this.index = args.index;
-        if (!this.index.getEntriesForRange) {
-            throw new Error('invalid arguments: not an index');
-        }
     }
     /**
      *

package/dist/indexedCramFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/rans/d04.js CHANGED Viewed

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = uncompress;
-//@ts-nocheck
+// @ts-nocheck
 const errors_1 = require("../errors");
 const constants_1 = require("./constants");
 const decoding_1 = __importDefault(require("./decoding"));

package/dist/rans/d04.js.map CHANGED Viewed

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package/dist/rans/d14.js CHANGED Viewed

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = uncompress;
-//@ts-nocheck
+// @ts-nocheck
 const constants_1 = require("./constants");
 const decoding_1 = __importDefault(require("./decoding"));
 function uncompress(

package/dist/rans/d14.js.map CHANGED Viewed

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package/dist/rans/decoding.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-//@ts-nocheck
+// @ts-nocheck
 const errors_1 = require("../errors");
 const constants_1 = require("./constants");
 class FC {

package/dist/rans/decoding.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/rans/frequencies.js CHANGED Viewed

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.readStatsO0 = readStatsO0;
 exports.readStatsO1 = readStatsO1;
-//@ts-nocheck
+// @ts-nocheck
 const errors_1 = require("../errors");
 const constants_1 = require("./constants");
 const decoding_1 = __importDefault(require("./decoding"));

package/dist/rans/frequencies.js.map CHANGED Viewed

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

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = uncompress;
-//@ts-nocheck
+// @ts-nocheck
 const buffer_1 = require("buffer");
 const errors_1 = require("../errors");
 const decoding_1 = __importDefault(require("./decoding"));

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

	@@ -1 +1 @@
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package/esm/craiIndex.d.ts CHANGED Viewed

@@ -6,9 +6,9 @@ export interface Slice {
     sliceStart: number;
     sliceBytes: number;
 }
-type ParsedIndex = Record<string, Slice[]>;
+type ParsedIndex = Record<string, Slice[] | undefined>;
 export default class CraiIndex {
-    private _parseCache;
+    private parseIndexP?;
     private filehandle;
     /**
      *
@@ -19,9 +19,7 @@ export default class CraiIndex {
      */
     constructor(args: CramFileSource);
     parseIndex(): Promise<ParsedIndex>;
-    getIndex(opts?: {
-        signal?: AbortSignal;
-    }): Promise<ParsedIndex>;
+    getIndex(): Promise<ParsedIndex>;
     /**
      * @param {number} seqId
      * @returns {Promise} true if the index contains entries for