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@gmod/cram

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@gmod/cram - npm Package Compare versions

Comparing version 1.7.1 to 1.7.2

4

CHANGELOG.md

@@ -0,1 +1,5 @@

# v1.7.2
- Update README.md with docs
# v1.7.1

@@ -2,0 +6,0 @@

4

dist/craiIndex.d.ts
import { CramFileSource } from './cramFile/file';
export declare type Slice = {
export type Slice = {
start: number;

@@ -9,3 +9,3 @@ span: number;

};
declare type ParsedIndex = Record<string, Slice[]>;
type ParsedIndex = Record<string, Slice[]>;
export default class CraiIndex {

@@ -12,0 +12,0 @@ private _parseCache;

6

dist/cramFile/codecs/_base.d.ts
import CramSlice from '../slice';
import { CramFileBlock } from '../file';
import { DataType } from './dataSeriesTypes';
export declare type DataTypeMapping = {
export type DataTypeMapping = {
byte: number;

@@ -10,7 +10,7 @@ int: number;

};
export declare type Cursor = {
export type Cursor = {
bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
bytePosition: number;
};
export declare type Cursors = {
export type Cursors = {
lastAlignmentStart: number;

@@ -17,0 +17,0 @@ coreBlock: Cursor;

2

dist/cramFile/codecs/byteArrayLength.d.ts

@@ -6,3 +6,3 @@ import CramCodec, { Cursors } from './_base';

import { DataType } from './dataSeriesTypes';
declare type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {

@@ -9,0 +9,0 @@ private instantiateCodec;

6

dist/cramFile/codecs/dataSeriesTypes.d.ts
import { CramEncoding } from '../encoding';
export declare type DataType = 'int' | 'byte' | 'long' | 'byteArray';
export declare type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
export declare type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;
export type DataType = 'int' | 'byte' | 'long' | 'byteArray';
export type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
export type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;

4

dist/cramFile/container/compressionScheme.d.ts

@@ -37,4 +37,4 @@ import CramCodec from '../codecs/_base';

};
export declare type DataSeriesTypes = typeof dataSeriesTypes;
declare type DataSeriesCache = {
export type DataSeriesTypes = typeof dataSeriesTypes;
type DataSeriesCache = {
[K in DataSeriesEncodingKey]?: CramCodec<DataSeriesTypes[K]>;

@@ -41,0 +41,0 @@ };

22

dist/cramFile/encoding.d.ts

@@ -1,2 +0,2 @@

export declare type NullEncoding = {
export type NullEncoding = {
codecId: 0;

@@ -6,3 +6,3 @@ parametersBytes: number;

};
export declare type ExternalCramEncoding = {
export type ExternalCramEncoding = {
codecId: 1;

@@ -14,3 +14,3 @@ parametersBytes: number;

};
export declare type GolombEncoding = {
export type GolombEncoding = {
codecId: 2;

@@ -23,3 +23,3 @@ parametersBytes: number;

};
export declare type HuffmanEncoding = {
export type HuffmanEncoding = {
codecId: 3;

@@ -34,3 +34,3 @@ parametersBytes: number;

};
export declare type ByteArrayLengthEncoding = {
export type ByteArrayLengthEncoding = {
codecId: 4;

@@ -43,3 +43,3 @@ parametersBytes: number;

};
export declare type ByteArrayStopCramEncoding = {
export type ByteArrayStopCramEncoding = {
codecId: 5;

@@ -52,3 +52,3 @@ parametersBytes: number;

};
export declare type BetaEncoding = {
export type BetaEncoding = {
codecId: 6;

@@ -61,3 +61,3 @@ parametersBytes: number;

};
export declare type SubexpEncoding = {
export type SubexpEncoding = {
codecId: 7;

@@ -70,3 +70,3 @@ parametersBytes: number;

};
export declare type GolombRiceEncoding = {
export type GolombRiceEncoding = {
codecId: 8;

@@ -79,3 +79,3 @@ parametersBytes: number;

};
export declare type GammaEncoding = {
export type GammaEncoding = {
codecId: 9;

@@ -87,2 +87,2 @@ parametersBytes: number;

};
export declare type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

8

dist/cramFile/file.d.ts

@@ -8,3 +8,3 @@ /// <reference types="node" />

import { Filehandle } from './filehandle';
export declare type CramFileSource = {
export type CramFileSource = {
filehandle?: Filehandle;

@@ -14,4 +14,4 @@ url?: string;

};
export declare type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
export declare type CramFileArgs = CramFileSource & {
export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
export type CramFileArgs = CramFileSource & {
checkSequenceMD5: boolean;

@@ -21,3 +21,3 @@ cacheSize?: number;

};
export declare type CramFileBlock = BlockHeader & {
export type CramFileBlock = BlockHeader & {
_endPosition: number;

@@ -24,0 +24,0 @@ contentPosition: number;

10

dist/cramFile/record.d.ts
import CramContainerCompressionScheme from './container/compressionScheme';
import decodeRecord from './slice/decodeRecord';
export declare type RefRegion = {
export type RefRegion = {
start: number;

@@ -8,3 +8,3 @@ end: number;

};
export declare type ReadFeature = {
export type ReadFeature = {
code: string;

@@ -17,3 +17,3 @@ pos: number;

};
export declare type MateRecord = {
export type MateRecord = {
readName?: string;

@@ -28,6 +28,6 @@ sequenceId: number;

export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];
declare type FlagsDecoder<Type> = {
type FlagsDecoder<Type> = {
[Property in Type as `is${Capitalize<string & Property>}`]: (flags: number) => boolean;
};
declare type FlagsEncoder<Type> = {
type FlagsEncoder<Type> = {
[Property in Type as `set${Capitalize<string & Property>}`]: (flags: number) => number;

@@ -34,0 +34,0 @@ };

14

dist/cramFile/sectionParsers.d.ts

@@ -10,4 +10,4 @@ import { Parser } from '@gmod/binary-parser';

};
export declare type CramTagDictionary = string[][];
export declare type CramPreservationMap = {
export type CramTagDictionary = string[][];
export type CramPreservationMap = {
MI: boolean;

@@ -22,3 +22,3 @@ UI: boolean;

};
export declare type MappedSliceHeader = {
export type MappedSliceHeader = {
refSeqId: number;

@@ -35,3 +35,3 @@ refSeqStart: number;

};
export declare type UnmappedSliceHeader = {
export type UnmappedSliceHeader = {
numRecords: number;

@@ -45,4 +45,4 @@ recordCounter: number;

export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
export declare type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
export declare type BlockHeader = {
export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
export type BlockHeader = {
compressionMethod: CompressionMethod;

@@ -54,3 +54,3 @@ contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';

};
export declare type CramCompressionHeader = ParsedItem<{
export type CramCompressionHeader = ParsedItem<{
preservation: CramPreservationMap;

@@ -57,0 +57,0 @@ dataSeriesEncoding: DataSeriesEncodingMap;

2

dist/cramFile/slice/decodeRecord.d.ts

@@ -7,3 +7,3 @@ import { ReadFeature } from '../record';

import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
export declare type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
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): {

@@ -10,0 +10,0 @@ readLength: number;

2

dist/cramFile/slice/index.d.ts

@@ -5,3 +5,3 @@ import CramRecord from '../record';

import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
export declare type SliceHeader = CramFileBlock & {
export type SliceHeader = CramFileBlock & {
parsedContent: MappedSliceHeader | UnmappedSliceHeader;

@@ -8,0 +8,0 @@ };

2

dist/cramFile/util.d.ts

@@ -5,3 +5,3 @@ /// <reference types="node" />

export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
export declare type ParsedItem<T> = T & {
export type ParsedItem<T> = T & {
_endPosition: number;

@@ -8,0 +8,0 @@ _size: number;

4

dist/indexedCramFile.d.ts

@@ -6,3 +6,3 @@ import CramFile from './cramFile';

import { Slice } from './craiIndex';
export declare type CramFileSource = {
export type CramFileSource = {
cramFilehandle?: Filehandle;

@@ -12,3 +12,3 @@ cramUrl?: string;

};
export declare type CramIndexLike = {
export type CramIndexLike = {
getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;

@@ -15,0 +15,0 @@ hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;

2

dist/sam.d.ts

@@ -1,2 +0,2 @@

export declare type HeaderDataItem = {
export type HeaderDataItem = {
tag: string;

@@ -3,0 +3,0 @@ data: Array<{

4

dist/typescript.d.ts
export declare function ensureNotNullish<T>(x: T | null | undefined): T;
export declare type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
export declare type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
export type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
export type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;

4

esm/craiIndex.d.ts
import { CramFileSource } from './cramFile/file';
export declare type Slice = {
export type Slice = {
start: number;

@@ -9,3 +9,3 @@ span: number;

};
declare type ParsedIndex = Record<string, Slice[]>;
type ParsedIndex = Record<string, Slice[]>;
export default class CraiIndex {

@@ -12,0 +12,0 @@ private _parseCache;

6

esm/cramFile/codecs/_base.d.ts
import CramSlice from '../slice';
import { CramFileBlock } from '../file';
import { DataType } from './dataSeriesTypes';
export declare type DataTypeMapping = {
export type DataTypeMapping = {
byte: number;

@@ -10,7 +10,7 @@ int: number;

};
export declare type Cursor = {
export type Cursor = {
bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
bytePosition: number;
};
export declare type Cursors = {
export type Cursors = {
lastAlignmentStart: number;

@@ -17,0 +17,0 @@ coreBlock: Cursor;

2

esm/cramFile/codecs/byteArrayLength.d.ts

@@ -6,3 +6,3 @@ import CramCodec, { Cursors } from './_base';

import { DataType } from './dataSeriesTypes';
declare type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {

@@ -9,0 +9,0 @@ private instantiateCodec;

6

esm/cramFile/codecs/dataSeriesTypes.d.ts
import { CramEncoding } from '../encoding';
export declare type DataType = 'int' | 'byte' | 'long' | 'byteArray';
export declare type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
export declare type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;
export type DataType = 'int' | 'byte' | 'long' | 'byteArray';
export type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
export type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;

4

esm/cramFile/container/compressionScheme.d.ts

@@ -37,4 +37,4 @@ import CramCodec from '../codecs/_base';

};
export declare type DataSeriesTypes = typeof dataSeriesTypes;
declare type DataSeriesCache = {
export type DataSeriesTypes = typeof dataSeriesTypes;
type DataSeriesCache = {
[K in DataSeriesEncodingKey]?: CramCodec<DataSeriesTypes[K]>;

@@ -41,0 +41,0 @@ };

22

esm/cramFile/encoding.d.ts

@@ -1,2 +0,2 @@

export declare type NullEncoding = {
export type NullEncoding = {
codecId: 0;

@@ -6,3 +6,3 @@ parametersBytes: number;

};
export declare type ExternalCramEncoding = {
export type ExternalCramEncoding = {
codecId: 1;

@@ -14,3 +14,3 @@ parametersBytes: number;

};
export declare type GolombEncoding = {
export type GolombEncoding = {
codecId: 2;

@@ -23,3 +23,3 @@ parametersBytes: number;

};
export declare type HuffmanEncoding = {
export type HuffmanEncoding = {
codecId: 3;

@@ -34,3 +34,3 @@ parametersBytes: number;

};
export declare type ByteArrayLengthEncoding = {
export type ByteArrayLengthEncoding = {
codecId: 4;

@@ -43,3 +43,3 @@ parametersBytes: number;

};
export declare type ByteArrayStopCramEncoding = {
export type ByteArrayStopCramEncoding = {
codecId: 5;

@@ -52,3 +52,3 @@ parametersBytes: number;

};
export declare type BetaEncoding = {
export type BetaEncoding = {
codecId: 6;

@@ -61,3 +61,3 @@ parametersBytes: number;

};
export declare type SubexpEncoding = {
export type SubexpEncoding = {
codecId: 7;

@@ -70,3 +70,3 @@ parametersBytes: number;

};
export declare type GolombRiceEncoding = {
export type GolombRiceEncoding = {
codecId: 8;

@@ -79,3 +79,3 @@ parametersBytes: number;

};
export declare type GammaEncoding = {
export type GammaEncoding = {
codecId: 9;

@@ -87,2 +87,2 @@ parametersBytes: number;

};
export declare type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

8

esm/cramFile/file.d.ts

@@ -8,3 +8,3 @@ /// <reference types="node" />

import { Filehandle } from './filehandle';
export declare type CramFileSource = {
export type CramFileSource = {
filehandle?: Filehandle;

@@ -14,4 +14,4 @@ url?: string;

};
export declare type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
export declare type CramFileArgs = CramFileSource & {
export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
export type CramFileArgs = CramFileSource & {
checkSequenceMD5: boolean;

@@ -21,3 +21,3 @@ cacheSize?: number;

};
export declare type CramFileBlock = BlockHeader & {
export type CramFileBlock = BlockHeader & {
_endPosition: number;

@@ -24,0 +24,0 @@ contentPosition: number;

10

esm/cramFile/record.d.ts
import CramContainerCompressionScheme from './container/compressionScheme';
import decodeRecord from './slice/decodeRecord';
export declare type RefRegion = {
export type RefRegion = {
start: number;

@@ -8,3 +8,3 @@ end: number;

};
export declare type ReadFeature = {
export type ReadFeature = {
code: string;

@@ -17,3 +17,3 @@ pos: number;

};
export declare type MateRecord = {
export type MateRecord = {
readName?: string;

@@ -28,6 +28,6 @@ sequenceId: number;

export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];
declare type FlagsDecoder<Type> = {
type FlagsDecoder<Type> = {
[Property in Type as `is${Capitalize<string & Property>}`]: (flags: number) => boolean;
};
declare type FlagsEncoder<Type> = {
type FlagsEncoder<Type> = {
[Property in Type as `set${Capitalize<string & Property>}`]: (flags: number) => number;

@@ -34,0 +34,0 @@ };

14

esm/cramFile/sectionParsers.d.ts

@@ -10,4 +10,4 @@ import { Parser } from '@gmod/binary-parser';

};
export declare type CramTagDictionary = string[][];
export declare type CramPreservationMap = {
export type CramTagDictionary = string[][];
export type CramPreservationMap = {
MI: boolean;

@@ -22,3 +22,3 @@ UI: boolean;

};
export declare type MappedSliceHeader = {
export type MappedSliceHeader = {
refSeqId: number;

@@ -35,3 +35,3 @@ refSeqStart: number;

};
export declare type UnmappedSliceHeader = {
export type UnmappedSliceHeader = {
numRecords: number;

@@ -45,4 +45,4 @@ recordCounter: number;

export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
export declare type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
export declare type BlockHeader = {
export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
export type BlockHeader = {
compressionMethod: CompressionMethod;

@@ -54,3 +54,3 @@ contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';

};
export declare type CramCompressionHeader = ParsedItem<{
export type CramCompressionHeader = ParsedItem<{
preservation: CramPreservationMap;

@@ -57,0 +57,0 @@ dataSeriesEncoding: DataSeriesEncodingMap;

2

esm/cramFile/slice/decodeRecord.d.ts

@@ -7,3 +7,3 @@ import { ReadFeature } from '../record';

import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
export declare type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
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): {

@@ -10,0 +10,0 @@ readLength: number;

2

esm/cramFile/slice/index.d.ts

@@ -5,3 +5,3 @@ import CramRecord from '../record';

import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
export declare type SliceHeader = CramFileBlock & {
export type SliceHeader = CramFileBlock & {
parsedContent: MappedSliceHeader | UnmappedSliceHeader;

@@ -8,0 +8,0 @@ };

2

esm/cramFile/util.d.ts

@@ -5,3 +5,3 @@ /// <reference types="node" />

export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
export declare type ParsedItem<T> = T & {
export type ParsedItem<T> = T & {
_endPosition: number;

@@ -8,0 +8,0 @@ _size: number;

4

esm/indexedCramFile.d.ts

@@ -6,3 +6,3 @@ import CramFile from './cramFile';

import { Slice } from './craiIndex';
export declare type CramFileSource = {
export type CramFileSource = {
cramFilehandle?: Filehandle;

@@ -12,3 +12,3 @@ cramUrl?: string;

};
export declare type CramIndexLike = {
export type CramIndexLike = {
getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;

@@ -15,0 +15,0 @@ hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;

2

esm/sam.d.ts

@@ -1,2 +0,2 @@

export declare type HeaderDataItem = {
export type HeaderDataItem = {
tag: string;

@@ -3,0 +3,0 @@ data: Array<{

4

esm/typescript.d.ts
export declare function ensureNotNullish<T>(x: T | null | undefined): T;
export declare type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
export declare type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
export type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
export type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;

28

package.json
{
"name": "@gmod/cram",
"version": "1.7.1",
"version": "1.7.2",
"description": "read CRAM files with pure Javascript",

@@ -60,12 +60,12 @@ "license": "MIT",

"@gmod/indexedfasta": "^2.0.2",
"@types/buffer-crc32": "^0.2.0",
"@types/jest": "^27.4.0",
"@types/buffer-crc32": "^0.2.2",
"@types/jest": "^29.2.4",
"@types/long": "^4.0.2",
"@types/md5": "^2.3.2",
"@types/pako": "^1.0.3",
"@typescript-eslint/eslint-plugin": "^5.9.1",
"@typescript-eslint/parser": "^5.9.1",
"@typescript-eslint/eslint-plugin": "^5.46.1",
"@typescript-eslint/parser": "^5.46.1",
"buffer": "^6.0.3",
"documentation": "^13.2.5",
"eslint": "^8.15.0",
"documentation": "^14.0.1",
"eslint": "^8.30.0",
"eslint-config-prettier": "^8.5.0",

@@ -75,11 +75,11 @@ "eslint-plugin-import": "^2.25.4",

"glob": "^8.0.3",
"jest": "^28.1.0",
"mock-fs": "^5.1.2",
"prettier": "^2.5.1",
"jest": "^29.3.1",
"mock-fs": "^5.2.0",
"prettier": "^2.8.1",
"rimraf": "^3.0.2",
"ts-jest": "^28.0.2",
"typescript": "^4.5.4",
"ts-jest": "^29.0.3",
"typescript": "^4.9.4",
"url": "^0.11.0",
"webpack": "5.72.1",
"webpack-cli": "^4.9.2"
"webpack": "5.75.0",
"webpack-cli": "^5.0.1"
},

@@ -86,0 +86,0 @@ "publishConfig": {

259

README.md

@@ -5,10 +5,10 @@ # @gmod/cram

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Read CRAM files (indexed or unindexed) with pure JS, works in node or in the browser.
- Reads CRAM 3.x and 2.x (3.1 added in v1.6.0)
- Does not read CRAM 1.x
- Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types
- Does implement bzip2 but not lzma codecs (yet); if this is important to your use case, please file an issue
* Reads CRAM 3.x and 2.x (3.1 added in v1.6.0)
* Does not read CRAM 1.x
* Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types
* Does implement bzip2 but not lzma codecs (yet); if this is important to your use case, please file an issue

@@ -126,8 +126,8 @@ ## Install

- [CramRecord](#cramrecord) - format of CRAM records returned by this API
- [ReadFeatures](#readfeatures) - format of read features on records
- [IndexedCramFile](#indexedcramfile) - indexed access into a CRAM file
- [CramFile](#cramfile) - .cram API
- [CraiIndex](#craiindex) - .crai index API
- [Error Classes](#error-classes) - special error classes thrown by this API
* [CramRecord](#cramrecord) - format of CRAM records returned by this API
* [ReadFeatures](#readfeatures) - format of read features on records
* [IndexedCramFile](#indexedcramfile) - indexed access into a CRAM file
* [CramFile](#cramfile) - .cram API
* [CraiIndex](#craiindex) - .crai index API
* [Error Classes](#error-classes) - special error classes thrown by this API

@@ -138,125 +138,4 @@ ### CramRecord

##### Table of Contents
#### Table of Contents
- [CramRecord](#cramrecord)
- [isPaired](#ispaired)
- [isProperlyPaired](#isproperlypaired)
- [isSegmentUnmapped](#issegmentunmapped)
- [isMateUnmapped](#ismateunmapped)
- [isReverseComplemented](#isreversecomplemented)
- [isMateReverseComplemented](#ismatereversecomplemented)
- [isRead1](#isread1)
- [isRead2](#isread2)
- [isSecondary](#issecondary)
- [isFailedQc](#isfailedqc)
- [isDuplicate](#isduplicate)
- [isSupplementary](#issupplementary)
- [isDetached](#isdetached)
- [hasMateDownStream](#hasmatedownstream)
- [isPreservingQualityScores](#ispreservingqualityscores)
- [isUnknownBases](#isunknownbases)
- [getReadBases](#getreadbases)
- [getPairOrientation](#getpairorientation)
- [addReferenceSequence](#addreferencesequence)
- [Parameters](#parameters)
#### CramRecord
Class of each CRAM record returned by this API.
##### isPaired
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is paired, regardless of whether both segments are mapped
##### isProperlyPaired
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is paired, and both segments are mapped
##### isSegmentUnmapped
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read itself is unmapped; conflictive with isProperlyPaired
##### isMateUnmapped
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read itself is unmapped; conflictive with isProperlyPaired
##### isReverseComplemented
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is mapped to the reverse strand
##### isMateReverseComplemented
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the mate is mapped to the reverse strand
##### isRead1
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is read number 1 in a pair
##### isRead2
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is read number 2 in a pair
##### isSecondary
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is a secondary alignment
##### isFailedQc
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this read has failed QC checks
##### isDuplicate
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is an optical or PCR duplicate
##### isSupplementary
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if this is a supplementary alignment
##### isDetached
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read is detached
##### hasMateDownStream
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read has a mate in this same CRAM segment
##### isPreservingQualityScores
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read contains qual scores
##### isUnknownBases
Returns **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** true if the read has no sequence bases
##### getReadBases
Get the original sequence of this read.
Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** sequence basepairs
##### getPairOrientation
Get the pair orientation of a paired read. Adapted from igv.js
Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** of paired orientatin
##### addReferenceSequence
Annotates this feature with the given reference sequence basepair
information. This will add a `sub` and a `ref` item to base
subsitution read features given the actual substituted and reference
base pairs, and will make the `getReadSequence()` method work.
###### Parameters
- `refRegion` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
- `refRegion.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
- `refRegion.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
- `refRegion.seq` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
- `compressionScheme` **CramContainerCompressionScheme**
Returns **[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)** nothing
### ReadFeatures

@@ -268,6 +147,6 @@

- **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings.
- **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code.
- **pos** (`number`): location relative to the read (1-based)
- **refPos** (`number`): location relative to the reference (1-based)
* **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings.
* **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code.
* **pos** (`number`): location relative to the read (1-based)
* **refPos** (`number`): location relative to the reference (1-based)

@@ -278,42 +157,4 @@ ### IndexedCramFile

##### Table of Contents
#### Table of Contents
- [constructor](#constructor)
- [Parameters](#parameters)
- [getRecordsForRange](#getrecordsforrange)
- [Parameters](#parameters-1)
- [hasDataForReferenceSequence](#hasdataforreferencesequence)
- [Parameters](#parameters-2)
#### constructor
##### Parameters
- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
- `args.cram` **CramFile**
- `args.index` **Index-like** object that supports getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]]
- `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache. default 20,000
- `args.fetchSizeLimit` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB.
- `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
#### getRecordsForRange
##### Parameters
- `seq` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** numeric ID of the reference sequence
- `start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of the range of interest. 1-based closed coordinates.
- `end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of the range of interest. 1-based closed coordinates.
- `opts` (optional, default `{}`)
#### hasDataForReferenceSequence
##### Parameters
- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the CRAM file contains data for the given
reference sequence numerical ID
### CramFile

@@ -323,26 +164,4 @@

##### Table of Contents
#### Table of Contents
- [constructor](#constructor)
- [Parameters](#parameters)
- [containerCount](#containercount)
#### constructor
##### Parameters
- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
- `args.filehandle` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** a filehandle that implements the stat() and
read() methods of the Node filehandle API <https://nodejs.org/api/fs.html#fs_class_filehandle>
- `args.path` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** path to the cram file
- `args.url` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** url for the cram file. also supports file:// urls for local files
- `args.seqFetch` **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?** a function with signature
`(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
- `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache. default 20,000
- `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
#### containerCount
### CraiIndex

@@ -352,44 +171,4 @@

##### Table of Contents
#### Table of Contents
- [constructor](#constructor)
- [Parameters](#parameters)
- [hasDataForReferenceSequence](#hasdataforreferencesequence)
- [Parameters](#parameters-1)
- [getEntriesForRange](#getentriesforrange)
- [Parameters](#parameters-2)
#### constructor
##### Parameters
- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
- `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
- `args.url` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
- `args.filehandle` **FileHandle?**
#### hasDataForReferenceSequence
##### Parameters
- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the index contains entries for
the given reference sequence ID, false otherwise
#### getEntriesForRange
fetch index entries for the given range
##### Parameters
- `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
- `queryStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
- `queryEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** promise for
an array of objects of the form
`{start, span, containerStart, sliceStart, sliceBytes }`
### CramUnimplementedError

@@ -396,0 +175,0 @@ 

dist/cram-bundle.js

Sorry, the diff of this file is too big to display

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