npm - @gmod/cram - Versions diffs - 3.0.0 → 3.0.1 - Mend

@gmod/cram 3.0.0 → 3.0.1

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 (65) hide show

package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/byteArrayStop.js +1 -1
package/dist/cramFile/codecs/huffman.js +1 -1
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/index.d.ts +1 -0
package/dist/cramFile/container/index.js +8 -5
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +1 -0
package/dist/cramFile/file.js +14 -13
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js +2 -2
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +5 -4
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js +2 -2
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/decoding.d.ts +4 -4
package/dist/rans/decoding.js +5 -6
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/index.js +4 -3
package/dist/rans/index.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.js +1 -1
package/esm/cramFile/codecs/huffman.js +1 -1
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/index.d.ts +1 -0
package/esm/cramFile/container/index.js +6 -3
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +1 -0
package/esm/cramFile/file.js +6 -5
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js +2 -2
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +5 -4
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js +2 -2
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.js +3 -3
package/esm/cramFile/util.js.map +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/decoding.d.ts +4 -4
package/esm/rans/decoding.js +5 -6
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/index.js +3 -2
package/esm/rans/index.js.map +1 -1
package/package.json +1 -1
package/src/cramFile/codecs/byteArrayStop.ts +1 -1
package/src/cramFile/codecs/huffman.ts +1 -1
package/src/cramFile/codecs/subexp.ts +2 -2
package/src/cramFile/container/index.ts +6 -6
package/src/cramFile/declare.d.ts +1 -0
package/src/cramFile/file.ts +10 -11
package/src/cramFile/record.ts +3 -6
package/src/cramFile/sectionParsers.ts +4 -4
package/src/cramFile/slice/decodeRecord.ts +20 -12
package/src/cramFile/slice/index.ts +2 -2
package/src/cramFile/util.ts +5 -5
package/src/rans/d04.ts +1 -1
package/src/rans/decoding.ts +5 -7
package/src/rans/index.ts +3 -2

package/esm/cramFile/sectionParsers.js.map CHANGED Viewed

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

@@ -65,7 +65,7 @@ function parseTagValueArray(buffer) {
         }
     }
     else {
-        throw new Error('unknown type: ' + arrayType);
+        throw new Error(`unknown type: ${arrayType}`);
     }
     return array;
 }
@@ -203,8 +203,8 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
     let mateRecordNumber;
     // mate record
     if (CramFlagsDecoder.isDetached(cramFlags)) {
-        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-        // const mate: any = {}
+        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't
+        // matter for javascript
         const mateFlags = decodeDataSeries('MF');
         let mateReadName;
         if (!compressionScheme.readNamesIncluded) {
@@ -268,7 +268,8 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
         if (readFeatureCount) {
             readFeatures = decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
         }
-        // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+        // compute the read's true span on the reference sequence, and the end
+        // coordinate of the alignment on the reference
         lengthOnRef = readLength;
         if (readFeatures) {
             for (const { code, data } of readFeatures) {

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

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

@@ -121,7 +121,7 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     }
     // delete this last because it's used by the
     // complicated template length estimation
-    delete thisRecord.mateRecordNumber;
+    thisRecord.mateRecordNumber = undefined;
 }
 export default class CramSlice {
     constructor(container, containerPosition, _unused) {
@@ -368,7 +368,7 @@ export default class CramSlice {
                         refRegion = {
                             id: seqId,
                             start: record.alignmentStart,
-                            end: -Infinity,
+                            end: Number.NEGATIVE_INFINITY,
                             seq: null,
                         };
                         refRegions[seqId] = refRegion;

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

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

@@ -91,7 +91,7 @@ export function parseLtf8(buffer, initialOffset) {
     }
     else if (countFlags < 0xf8) {
         n =
-            ((buffer[offset] & 15) * Math.pow(2, 32) + (buffer[offset + 1] << 24)) |
+            ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
                 ((buffer[offset + 2] << 16) |
                     (buffer[offset + 3] << 8) |
                     buffer[offset + 4]);
@@ -100,7 +100,7 @@ export function parseLtf8(buffer, initialOffset) {
     }
     else if (countFlags < 0xfc) {
         n =
-            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2, 32) +
+            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
                 (buffer[offset + 2] << 24)) |
                 ((buffer[offset + 3] << 16) |
                     (buffer[offset + 4] << 8) |
@@ -112,7 +112,7 @@ export function parseLtf8(buffer, initialOffset) {
             ((((buffer[offset] & 3) << 16) |
                 (buffer[offset + 1] << 8) |
                 buffer[offset + 2]) *
-                Math.pow(2, 32) +
+                2 ** 32 +
                 (buffer[offset + 3] << 24)) |
                 ((buffer[offset + 4] << 16) |
                     (buffer[offset + 5] << 8) |

package/esm/cramFile/util.js.map CHANGED Viewed

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

@@ -4,7 +4,7 @@ declare class FC {
 declare class AriDecoder {
     constructor();
 }
-declare class Symbol {
+declare class DecodingSymbol {
     constructor();
 }
 declare function symbolInit(sym: any, start: any, freq: any): void;
@@ -13,10 +13,10 @@ declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
 declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
 declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
 declare function renormalize(r: any, pptr: any): any;
-declare const Decode: {
+declare const _default: {
     FC: typeof FC;
     AriDecoder: typeof AriDecoder;
-    Symbol: typeof Symbol;
+    DecodingSymbol: typeof DecodingSymbol;
     symbolInit: typeof symbolInit;
     advanceStep: typeof advanceStep;
     advanceSymbolStep: typeof advanceSymbolStep;
@@ -24,4 +24,4 @@ declare const Decode: {
     advanceSymbol: typeof advanceSymbol;
     renormalize: typeof renormalize;
 };
-export default Decode;
+export default _default;

package/esm/rans/decoding.js CHANGED Viewed

@@ -19,7 +19,7 @@ class AriDecoder {
         this.R = null;
     }
 }
-class Symbol {
+class DecodingSymbol {
     // int start; // Start of range.
     // int freq; // Symbol frequency.
     constructor() {
@@ -30,10 +30,10 @@ class Symbol {
 // Initialize a decoder symbol to start "start" and frequency "freq"
 function symbolInit(sym, start, freq) {
     if (!(start <= 1 << 16)) {
-        throw new CramMalformedError(`assertion failed: start <= 1<<16`);
+        throw new CramMalformedError('assertion failed: start <= 1<<16');
     }
     if (!(freq <= (1 << 16) - start)) {
-        throw new CramMalformedError(`assertion failed: freq <= 1<<16`);
+        throw new CramMalformedError('assertion failed: freq <= 1<<16');
     }
     sym.start = start;
     sym.freq = freq;
@@ -104,10 +104,10 @@ function symbolInit(sym, start, freq) {
     }
     return r;
 }
-const Decode = {
+export default {
     FC,
     AriDecoder,
-    Symbol,
+    DecodingSymbol,
     symbolInit,
     advanceStep,
     advanceSymbolStep,
@@ -115,5 +115,4 @@ const Decode = {
     advanceSymbol,
     renormalize,
 };
-export default Decode;
 //# sourceMappingURL=decoding.js.map

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

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

@@ -1,4 +1,5 @@
 //@ts-nocheck
+import { Buffer } from 'buffer';
 import { CramMalformedError } from '../errors';
 import Decoding from './decoding';
 import { readStatsO0, readStatsO1 } from './frequencies';
@@ -95,7 +96,7 @@ function uncompressOrder0Way4(
     const D = new Decoding.AriDecoder();
     const syms = new Array(256);
     for (let i = 0; i < syms.length; i += 1) {
-        syms[i] = new Decoding.Symbol();
+        syms[i] = new Decoding.DecodingSymbol();
     }
     readStatsO0(input, D, syms);
     D04(input, D, syms, out);
@@ -112,7 +113,7 @@ function uncompressOrder1Way4(
     for (let i = 0; i < syms.length; i += 1) {
         syms[i] = new Array(256);
         for (let j = 0; j < syms[i].length; j += 1) {
-            syms[i][j] = new Decoding.Symbol();
+            syms[i][j] = new Decoding.DecodingSymbol();
         }
     }
     readStatsO1(input, D, syms);

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

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "3.0.0",
+  "version": "3.0.1",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",

package/src/cramFile/codecs/byteArrayStop.ts CHANGED Viewed

@@ -51,7 +51,7 @@ export default class ByteArrayStopCodec extends CramCodec<
     ) {
       if (stopPosition === dataBuffer.length) {
         throw new CramBufferOverrunError(
-          `byteArrayStop reading beyond length of data buffer?`,
+          'byteArrayStop reading beyond length of data buffer?',
         )
       }
       stopPosition = stopPosition + 1

package/src/cramFile/codecs/huffman.ts CHANGED Viewed

@@ -83,7 +83,7 @@ export default class HuffmanIntCodec extends CramCodec<
     let codeLength = 0
     let codeValue = -1
     Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
-      const bitLengthInt = parseInt(bitLength, 10)
+      const bitLengthInt = Number.parseInt(bitLength, 10)
       symbols.forEach(symbol => {
         const code = {
           bitLength: bitLengthInt,

package/src/cramFile/codecs/subexp.ts CHANGED Viewed

@@ -29,8 +29,8 @@ export default class SubexpCodec extends CramCodec<
       numLeadingOnes = numLeadingOnes + 1
     }
-    let b
-    let n
+    let b: number
+    let n: number
     if (numLeadingOnes === 0) {
       b = this.parameters.K
       n = getBits(coreDataBlock.content, cursors.coreBlock, b)

package/src/cramFile/container/index.ts CHANGED Viewed

@@ -1,5 +1,6 @@
+import { Buffer } from 'buffer'
 import { CramMalformedError } from '../../errors'
+// locals
 import { itf8Size, parseItem, tinyMemoize } from '../util'
 import CramSlice from '../slice'
 import CramContainerCompressionScheme from './compressionScheme'
@@ -33,7 +34,7 @@ export default class CramContainer {
     }
     if (block.contentType !== 'COMPRESSION_HEADER') {
       throw new CramMalformedError(
-        `invalid content type ${block.contentType} in what is supposed to be the compression header block`,
+        `invalid content type ${block.contentType} in compression header block`,
       )
     }
@@ -81,9 +82,7 @@ export default class CramContainer {
     const { size: fileSize } = await this.file.stat()
     if (position >= fileSize) {
-      console.warn(
-        `position:${position}>=fileSize:${fileSize} in cram container`,
-      )
+      console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`)
       return undefined
     }
@@ -94,8 +93,9 @@ export default class CramContainer {
     const header1 = parseItem(bytes1, cramContainerHeader1.parser)
     const numLandmarksSize = itf8Size(header1.numLandmarks)
     if (position + header1.length >= fileSize) {
+      // header indicates container goes beyond fileSize
       console.warn(
-        `container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
+        `container at ${position} is beyond fileSize:${fileSize}, skipping`,
       )
       return undefined
     }

package/src/cramFile/declare.d.ts ADDED Viewed

	@@ -0,0 +1 @@
1	+ declare module 'bzip2'