Class FastqParser

Streaming FASTQ parser with quality score handling

Hierarchy

AbstractParser<FastqSequence, FastqParserOptions>
- FastqParser

Index

Constructors

Methods

parseString parseMultiLineString parseFile parse

Constructors

constructor

new FastqParser(options?: FastqParserOptions): FastqParser
Parameters
- options: FastqParserOptions = {}
Returns FastqParser
Overrides AbstractParser<FastqSequence, FastqParserOptions>.constructor
- Defined in src/formats/fastq.ts:146

Methods

parseString

parseString(data: string): AsyncIterable<FastqSequence>
Parse FASTQ sequences from a string
Parameters
- data: string
Returns AsyncIterable<FastqSequence>
Overrides AbstractParser.parseString
- Defined in src/formats/fastq.ts:203

parseMultiLineString

parseMultiLineString(data: string): FastqSequence[]
Parse multi-line FASTQ sequences using state machine Provides full FASTQ specification compliance for wrapped sequences
Parameters
- data: string
Returns FastqSequence[]
- Defined in src/formats/fastq.ts:212

parseFile

parseFile(
filePath: string,
options?: FileReaderOptions,
): AsyncIterable<FastqSequence>
Parse FASTQ sequences from a file using streaming I/O
Parameters
- filePath: string
  Path to FASTQ file to parse
- Optionaloptions: FileReaderOptions
  File reading options for performance tuning
Returns AsyncIterable<FastqSequence>
Yields
FastqSequence objects as they are parsed from the file

Throws
When file cannot be read

Throws
When FASTQ format is invalid

Throws
When quality data is malformed
Example
```
const parser = new FastqParser();
for await (const sequence of parser.parseFile('/path/to/reads.fastq')) {
  console.log(`${sequence.id}: Q${sequence.qualityStats?.mean || 'unknown'}`);
}
```
Overrides AbstractParser.parseFile
- Defined in src/formats/fastq.ts:236

parse

parse(
stream: ReadableStream<Uint8Array<ArrayBufferLike>>,
): AsyncIterable<FastqSequence>
Parse FASTQ sequences from a ReadableStream
Parameters
- stream: ReadableStream<Uint8Array<ArrayBufferLike>>
Returns AsyncIterable<FastqSequence>
Overrides AbstractParser.parse
- Defined in src/formats/fastq.ts:274