@gmod/cram 3.0.7 → 4.0.0

package/dist/cramFile/record.js.map

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

@@ -2,7 +2,7 @@ import { TupleOf } from '../typescript';
 import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
 import { CramEncoding } from './encoding';
 export declare function cramFileDefinition(): {
-    parser: (buffer: Buffer, _startOffset?: number) => {
+    parser: (b: Uint8Array, _startOffset?: number) => {
         value: {
             magic: string;
             majorVersion: number;
@@ -14,7 +14,7 @@ export declare function cramFileDefinition(): {
     maxLength: number;
 };
 export declare function cramBlockHeader(): {
-    parser: (buffer: Buffer, _startOffset?: number) => {
+    parser: (buffer: Uint8Array, _startOffset?: number) => {
         offset: number;
         value: {
             uncompressedSize: number;
@@ -27,7 +27,7 @@ export declare function cramBlockHeader(): {
     maxLength: number;
 };
 export declare function cramBlockCrc32(): {
-    parser: (buffer: Buffer, offset: number) => {
+    parser: (buffer: Uint8Array, offset: number) => {
         offset: number;
         value: {
             crc32: number;
@@ -37,7 +37,7 @@ export declare function cramBlockCrc32(): {
 };
 export type CramTagDictionary = string[][];
 export declare function cramTagDictionary(): {
-    parser: (buffer: Buffer, offset: number) => {
+    parser: (buffer: Uint8Array, offset: number) => {
         value: {
             size: number;
             ents: string[][];
@@ -56,7 +56,7 @@ export interface CramPreservationMap {
     TD: CramTagDictionary;
 }
 export declare function cramPreservationMap(): {
-    parser: (buffer: Buffer, offset: number) => {
+    parser: (buffer: Uint8Array, offset: number) => {
         value: {
             mapSize: number;
             mapCount: number;
@@ -117,7 +117,7 @@ export interface CramCompressionHeader {
 }
 export declare function getSectionParsers(majorVersion: number): {
     cramFileDefinition: {
-        parser: (buffer: Buffer, _startOffset?: number) => {
+        parser: (b: Uint8Array, _startOffset?: number) => {
             value: {
                 magic: string;
                 majorVersion: number;
@@ -129,7 +129,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: number;
     };
     cramBlockHeader: {
-        parser: (buffer: Buffer, _startOffset?: number) => {
+        parser: (buffer: Uint8Array, _startOffset?: number) => {
             offset: number;
             value: {
                 uncompressedSize: number;
@@ -142,7 +142,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: number;
     };
     cramBlockCrc32: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             offset: number;
             value: {
                 crc32: number;
@@ -151,7 +151,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: number;
     };
     cramDataSeriesEncodingMap: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 mapSize: number;
                 ents: {
@@ -164,7 +164,7 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramTagEncodingMap: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 mapSize: number;
                 ents: {
@@ -177,7 +177,7 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramCompressionHeader: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 dataSeriesEncoding: DataSeriesEncodingMap;
                 preservation: CramPreservationMap;
@@ -187,13 +187,13 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramEncoding: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: Value;
             offset: number;
         };
     };
     cramUnmappedSliceHeader: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 recordCounter: number;
                 md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
@@ -207,7 +207,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: (numContentIds: number) => number;
     };
     cramMappedSliceHeader: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
                 numBlocks: number;
@@ -226,7 +226,7 @@ export declare function getSectionParsers(majorVersion: number): {
     };
     cramContainerHeader1: {
         maxLength: number;
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 length: number;
                 refSeqId: number;
@@ -242,7 +242,7 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramContainerHeader2: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 numLandmarks: number;
                 landmarks: number[];

package/dist/cramFile/sectionParsers.js

@@ -10,19 +10,18 @@ exports.getSectionParsers = getSectionParsers;
 const util_1 = require("./util");
 function cramFileDefinition() {
     return {
-        parser: (buffer, _startOffset = 0) => {
-            const b = buffer;
+        parser: (b, _startOffset = 0) => {
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+            const decoder = new TextDecoder('utf8');
             let offset = 0;
-            const magic = buffer.subarray(offset, offset + 4).toString();
+            const magic = decoder.decode(b.subarray(offset, offset + 4));
             offset += 4;
             const majorVersion = dataView.getUint8(offset);
             offset += 1;
             const minorVersion = dataView.getUint8(offset);
             offset += 1;
-            const fileId = b
-                .subarray(offset, offset + 20)
-                .toString()
+            const fileId = decoder
+                .decode(b.subarray(offset, offset + 20))
                 .replaceAll('\0', '');
             offset += 20;
             return {
@@ -109,7 +108,8 @@ function cramBlockCrc32() {
     };
 }
 function makeTagSet(buffer, stringStart, stringEnd) {
-    const str = buffer.toString('utf8', stringStart, stringEnd);
+    const decoder = new TextDecoder('utf8');
+    const str = decoder.decode(buffer.subarray(stringStart, stringEnd));
     const tags = [];
     for (let i = 0; i < str.length; i += 3) {
         tags.push(str.slice(i, i + 3));
@@ -633,8 +633,11 @@ function cramContainerHeader2(majorVersion) {
                 offset += 4;
             }
             return {
-                value: Object.assign(Object.assign({}, (crc32 === undefined ? {} : { crc32 })), { numLandmarks,
-                    landmarks }),
+                value: {
+                    ...(crc32 === undefined ? {} : { crc32 }),
+                    numLandmarks,
+                    landmarks,
+                },
                 offset,
             };
         },

package/dist/cramFile/sectionParsers.js.map

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

@@ -1,9 +1,9 @@
+import { Cursors, DataTypeMapping } from '../codecs/_base';
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
+import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme';
 import { ReadFeature } from '../record';
 import CramSlice, { SliceHeader } from './index';
-import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme';
 import { CramFileBlock } from '../file';
-import { Cursors, DataTypeMapping } from '../codecs/_base';
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
 export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
 export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
     readLength: number;

package/dist/cramFile/slice/decodeRecord.js

@@ -28,43 +28,43 @@ function parseTagValueArray(buffer) {
     buffer = buffer.slice(5);
     if (arrayType === 'c') {
         const arr = new Int8Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'C') {
         const arr = new Uint8Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 's') {
         const arr = new Int16Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'S') {
         const arr = new Uint16Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'i') {
         const arr = new Int32Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'I') {
         const arr = new Uint32Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
     else if (arrayType === 'f') {
         const arr = new Float32Array(buffer.buffer);
-        for (let i = 0; i < length; i += 1) {
+        for (let i = 0; i < length; i++) {
             array[i] = arr[i];
         }
     }
@@ -133,7 +133,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
         // }
         return data;
     }
-    for (let i = 0; i < readFeatureCount; i += 1) {
+    for (let i = 0; i < readFeatureCount; i++) {
         const code = String.fromCharCode(decodeDataSeries('FC'));
         const readPosDelta = decodeDataSeries('FP');
         // map of operator name -> data series name
@@ -250,7 +250,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     // TN = tag names
     const TN = compressionScheme.getTagNames(TLindex);
     const ntags = TN.length;
-    for (let i = 0; i < ntags; i += 1) {
+    for (let i = 0; i < ntags; i++) {
         const tagId = TN[i];
         const tagName = tagId.slice(0, 2);
         const tagType = tagId.slice(2, 3);
@@ -306,13 +306,13 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     }
     else {
         const bases = new Array(readLength);
-        for (let i = 0; i < bases.length; i += 1) {
+        for (let i = 0; i < bases.length; i++) {
             bases[i] = decodeDataSeries('BA');
         }
         readBases = String.fromCharCode(...bases);
         if (record_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
             qualityScores = new Array(readLength);
-            for (let i = 0; i < bases.length; i += 1) {
+            for (let i = 0; i < bases.length; i++) {
                 qualityScores[i] = decodeDataSeries('QS');
             }
         }

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

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

@@ -1,6 +1,6 @@
-import CramRecord from '../record';
 import CramContainer from '../container';
 import { CramFileBlock } from '../file';
+import CramRecord from '../record';
 import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
 export type SliceHeader = CramFileBlock & {
     parsedContent: MappedSliceHeader | UnmappedSliceHeader;
@@ -31,7 +31,7 @@ export default class CramSlice {
         _endPosition: number;
         contentPosition: number;
         _size: number;
-        content: Buffer;
+        content: Uint8Array;
         crc32?: number;
     }>;
     getBlocks(): Promise<CramFileBlock[]>;