@gmod/cram 3.0.6 → 4.0.0

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

@@ -25,43 +25,43 @@ 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];
         }
     }
@@ -130,7 +130,7 @@ 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
@@ -247,7 +247,7 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
     // 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);
@@ -303,13 +303,13 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
     }
     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 (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/esm/cramFile/slice/decodeRecord.js.map

@@ -1 +1 @@
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package/esm/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[]>;

package/esm/cramFile/slice/index.js

@@ -1,10 +1,10 @@
 import { CramArgumentError, CramMalformedError } from '../../errors';
-import { parseItem, sequenceMD5, tinyMemoize } from '../util';
+import { CramBufferOverrunError } from '../codecs/getBits';
 import Constants from '../constants';
 import decodeRecord from './decodeRecord';
 import CramRecord from '../record';
 import { getSectionParsers, isMappedSliceHeader, } from '../sectionParsers';
-import { CramBufferOverrunError } from '../codecs/getBits';
+import { parseItem, sequenceMD5, tinyMemoize } from '../util';
 /**
  * @private
  * Try to estimate the template length from a bunch of interrelated multi-segment reads.
@@ -241,7 +241,6 @@ export default class CramSlice {
         return this.getRecords(() => true);
     }
     async _fetchRecords() {
-        var _a, _b;
         const { majorVersion } = await this.file.getDefinition();
         const compressionScheme = await this.container.getCompressionScheme();
         if (compressionScheme === undefined) {
@@ -254,12 +253,14 @@ export default class CramSlice {
             this.file.options.checkSequenceMD5 &&
             isMappedSliceHeader(sliceHeader.parsedContent) &&
             sliceHeader.parsedContent.refSeqId >= 0 &&
-            ((_a = sliceHeader.parsedContent.md5) === null || _a === void 0 ? void 0 : _a.join('')) !== '0000000000000000') {
+            sliceHeader.parsedContent.md5?.join('') !== '0000000000000000') {
             const refRegion = await this.getReferenceRegion();
             if (refRegion) {
                 const { seq, start, end } = refRegion;
                 const seqMd5 = sequenceMD5(seq);
-                const storedMd5 = (_b = sliceHeader.parsedContent.md5) === null || _b === void 0 ? void 0 : _b.map(byte => (byte < 16 ? '0' : '') + byte.toString(16)).join('');
+                const storedMd5 = sliceHeader.parsedContent.md5
+                    ?.map(byte => (byte < 16 ? '0' : '') + byte.toString(16))
+                    .join('');
                 if (seqMd5 !== storedMd5) {
                     throw new CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
                 }
@@ -389,7 +390,7 @@ export default class CramSlice {
                 for (const record of records) {
                     const seqId = singleRefId !== undefined ? singleRefId : record.sequenceId;
                     const refRegion = refRegions[seqId];
-                    if (refRegion === null || refRegion === void 0 ? void 0 : refRegion.seq) {
+                    if (refRegion?.seq) {
                         const seq = refRegion.seq;
                         record.addReferenceSequence({ ...refRegion, seq }, compressionScheme);
                     }

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

@@ -1 +1 @@
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package/esm/cramFile/util.d.ts

@@ -1,7 +1,7 @@
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
 export declare function parseItf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
-export declare function parseLtf8(buffer: Buffer, initialOffset: number): readonly [number, number];
-export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, offset: number) => {
+export declare function parseLtf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
+export declare function parseItem<T>(buffer: Uint8Array, parser: (buffer: Uint8Array, offset: number) => {
     offset: number;
     value: T;
 }, startBufferPosition?: number, startFilePosition?: number): T & {
@@ -10,3 +10,5 @@ export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, of
 };
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;
+export declare function sum(array: Uint8Array[]): number;
+export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;

package/esm/cramFile/util.js

@@ -1,5 +1,5 @@
-import md5 from 'md5';
 import Long from 'long';
+import md5 from 'md5';
 import { CramBufferOverrunError } from './codecs/getBits';
 export function itf8Size(v) {
     if (!(v & ~0x7f)) {
@@ -60,6 +60,7 @@ export function parseItf8(buffer, initialOffset) {
     return [result, offset - initialOffset];
 }
 export function parseLtf8(buffer, initialOffset) {
+    const dataView = new DataView(buffer.buffer);
     let offset = initialOffset;
     const countFlags = buffer[offset];
     let n;
@@ -77,7 +78,7 @@ export function parseLtf8(buffer, initialOffset) {
                 (buffer[offset + 1] << 8) |
                 buffer[offset + 2]) &
                 0x1fffff;
-        n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1);
+        n = ((countFlags & 63) << 16) | dataView.getUint16(offset + 1, true);
         offset += 3;
     }
     else if (countFlags < 0xf0) {
@@ -168,4 +169,20 @@ export function tinyMemoize(_class, methodName) {
 export function sequenceMD5(seq) {
     return md5(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
+export function sum(array) {
+    let sum = 0;
+    for (const entry of array) {
+        sum += entry.length;
+    }
+    return sum;
+}
+export function concatUint8Array(args) {
+    const mergedArray = new Uint8Array(sum(args));
+    let offset = 0;
+    for (const entry of args) {
+        mergedArray.set(entry, offset);
+        offset += entry.length;
+    }
+    return mergedArray;
+}
 //# sourceMappingURL=util.js.map

package/esm/cramFile/util.js.map

@@ -1 +1 @@
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package/esm/htscodecs/arith_gen.d.ts

@@ -0,0 +1,18 @@
+export = RangeCoderGen;
+declare class RangeCoderGen {
+    decode(src: any): Uint8Array<any>;
+    stream: IOStream | undefined;
+    decodeStream(stream: any, n_out?: number): Uint8Array<any>;
+    decode0(stream: any, n_out: any): Uint8Array<any>;
+    decode1(stream: any, n_out: any): Uint8Array<any>;
+    decodeExt(stream: any, n_out: any): Uint8Array<ArrayBuffer>;
+    decodeRLE0(stream: any, n_out: any): Uint8Array<any>;
+    decodeRLE1(stream: any, n_out: any): Uint8Array<any>;
+    decodePackMeta(stream: any): any[];
+    nsym: any;
+    decodePack(data: any, M: any, len: any): any;
+    packMeta(src: any): (number | any[] | IOStream)[];
+    decodeStripe(stream: any, len: any): Uint8Array<any>;
+    decodeCat(stream: any, len: any): Uint8Array<any>;
+}
+import IOStream = require("./iostream");