IO Module API¶

Namespace: fq::io

FastqRecord¶

Zero-copy view of FASTQ record, using std::string_view pointing to continuous memory in FastqBatch.

Fields¶

Field	Type	Description
`id`	`std::string_view`	Record identifier
`sequence`	`std::string_view`	DNA sequence
`quality`	`std::string_view`	Quality score string
`separator`	`std::string_view`	Separator line (usually `+`)

Key Methods¶

auto averageQuality(int qualityEncoding = 33) const -> double;
auto length() const -> size_t;
auto gcContent() const -> double;
auto nRatio() const -> double;

FastqBatch¶

Container for batch storage of multiple FASTQ records, maintaining continuous memory buffer.

Key Methods¶

auto records() const -> const std::vector<FastqRecord>&;
auto size() const -> size_t;
auto empty() const -> bool;
void clear();
void reserve(size_t count);

Memory Model¶

FastqBatch
├── buffer_     Continuous memory block (stores raw text)
└── records_    FastqRecord array (string_view points to buffer_)

FastqReader¶

FASTQ file reader, supports plain text and gzip compressed formats.

Construction and Usage¶

fq::io::FastqReader reader("input.fastq.gz");

fq::io::FastqBatch batch;
while (reader.nextBatch(batch, 10000)) {
    for (const auto& record : batch.records()) {
        // Process each record
    }
}

Key Methods¶

explicit FastqReader(const std::string& path);
auto nextBatch(FastqBatch& batch, size_t batchSize = 10000) -> bool;
auto isOpen() const -> bool;

Performance Parameters¶

Parameter	Description
`readChunkBytes`	Bytes to read each time
`zlibBufferBytes`	zlib decompression buffer size
`maxBufferBytes`	Maximum buffer limit

FastqWriter¶

FASTQ file writer, supports plain text and gzip compressed output.

Construction and Usage¶

fq::io::FastqWriter writer("output.fastq.gz");

for (const auto& record : batch.records()) {
    writer.write(record);
}

Performance Parameters¶

Parameter	Description
`zlibBufferBytes`	Compression buffer size
`outputBufferBytes`	Output buffer size

FastqBatchPool¶

Object pool based on ObjectPool<FastqBatch>, reducing frequent allocations in TBB pipeline.

auto pool = fq::io::createFastqBatchPool(initialSize, maxSize);
auto batch = pool->acquire();  // Acquire from pool
// shared_ptr destructor automatically returns to pool