npm - @gmod/cram - Versions diffs - 3.0.4 → 3.0.6 - Mend

@gmod/cram 3.0.4 → 3.0.6

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 +2 -3
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 +9 -10
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 +9 -12
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 +2 -3
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 +9 -10
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 +9 -9
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 +9 -9
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 +9 -10
package/src/cramFile/record.ts +3 -10
package/src/cramFile/sectionParsers.ts +4 -4
package/src/cramFile/slice/decodeRecord.ts +25 -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/esm/cramFile/sectionParsers.js.map CHANGED Viewed

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package/esm/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -1,4 +1,3 @@
-import Long from 'long';
 import { CramMalformedError } from '../../errors';
 import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from '../record';
 import { isMappedSliceHeader } from '../sectionParsers';
@@ -19,7 +18,9 @@ function readNullTerminatedString(buffer) {
  */
 function parseTagValueArray(buffer) {
     const arrayType = String.fromCharCode(buffer[0]);
-    const length = Int32Array.from(buffer.slice(1))[0];
+    const dataView = new DataView(buffer.buffer);
+    const littleEndian = true;
+    const length = dataView.getUint32(1, littleEndian);
     const array = new Array(length);
     buffer = buffer.slice(5);
     if (arrayType === 'c') {
@@ -77,7 +78,7 @@ function parseTagData(tagType, buffer) {
         return String.fromCharCode(buffer[0]);
     }
     if (tagType === 'I') {
-        return Long.fromBytesLE(buffer).toNumber();
+        return new Uint32Array(buffer.buffer)[0];
     }
     if (tagType === 'i') {
         return new Int32Array(buffer.buffer)[0];
@@ -250,12 +251,11 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
         const tagId = TN[i];
         const tagName = tagId.slice(0, 2);
         const tagType = tagId.slice(2, 3);
-        const tagCodec = compressionScheme.getCodecForTag(tagId);
-        if (!tagCodec) {
-            throw new CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);
-        }
-        const tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-        tags[tagName] = parseTagData(tagType, tagData);
+        const tagData = compressionScheme
+            .getCodecForTag(tagId)
+            .decode(slice, coreDataBlock, blocksByContentId, cursors);
+        tags[tagName] =
+            typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData);
     }
     let readFeatures;
     let lengthOnRef;

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

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

@@ -55,14 +55,12 @@ 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 CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
-    }
     const complicatedMultiSegment = !!(mateRecord.mate ||
         (mateRecord.mateRecordNumber !== undefined &&
             mateRecord.mateRecordNumber !== currentRecordNumber));
@@ -124,9 +122,10 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     thisRecord.mateRecordNumber = undefined;
 }
 export default class CramSlice {
-    constructor(container, containerPosition, _unused) {
+    constructor(container, containerPosition, sliceSize) {
         this.container = container;
         this.containerPosition = containerPosition;
+        this.sliceSize = sliceSize;
         this.file = container.file;
     }
     // memoize
@@ -173,7 +172,6 @@ export default class CramSlice {
     // no memoize
     async getCoreDataBlock() {
         const blocks = await this.getBlocks();
-        // the core data block is always the first block in the slice
         return blocks[0];
     }
     // memoize
@@ -250,9 +248,6 @@ export default class CramSlice {
             throw new Error('compression scheme undefined');
         }
         const sliceHeader = await this.getHeader();
-        if (sliceHeader === undefined) {
-            throw new Error('slice header undefined');
-        }
         const blocksByContentId = await this._getBlocksContentIdIndex();
         // check MD5 of reference if available
         if (majorVersion > 1 &&
@@ -301,7 +296,7 @@ export default 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 = decodeRecord(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
@@ -316,7 +311,6 @@ export default class CramSlice {
             catch (e) {
                 if (e instanceof CramBufferOverrunError) {
                     console.warn('read attempted beyond end of buffer, file seems truncated.');
-                    records = records.filter(r => !!r);
                     break;
                 }
                 else {
@@ -406,7 +400,7 @@ export default class CramSlice {
     }
 }
 // memoize several methods in the class for performance
-'getHeader getBlocks _getBlocksContentIdIndex'
-    .split(' ')
-    .forEach(method => tinyMemoize(CramSlice, method));
+'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
+    tinyMemoize(CramSlice, method);
+});
 //# sourceMappingURL=index.js.map

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

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

@@ -26,9 +26,6 @@ export default 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/esm/indexedCramFile.js.map CHANGED Viewed

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

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors';
 import { TF_SHIFT } from './constants';
 import Decoding from './decoding';

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

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package/esm/rans/d14.js CHANGED Viewed

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { TF_SHIFT } from './constants';
 import Decoding from './decoding';
 export default function uncompress(

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package/esm/rans/decoding.js CHANGED Viewed

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors';
 import { RANS_BYTE_L } from './constants';
 class FC {

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

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package/esm/rans/frequencies.js CHANGED Viewed

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors';
 import { TOTFREQ } from './constants';
 import Decoding from './decoding';

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

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

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { Buffer } from 'buffer';
 import { CramMalformedError } from '../errors';
 import Decoding from './decoding';

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

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