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API Overview

FastQTools provides a clean C++ public API, ready for library-level integration into other projects.

Entry Header

#include <fqtools/fq.h>

fq.h aggregates all public interface headers, including:

Module Header Description
IO <fqtools/io/...> FASTQ read/write (FastqReader, FastqWriter, FastqRecord, FastqBatch)
Processing <fqtools/processing/...> Processing pipeline, Predicate, Mutator
Statistics <fqtools/statistics/...> Statistics computation interface
Core <fqtools/core/core.h> Sequence utility functions
Config <fqtools/config/config.h> Configuration management
Error <fqtools/error/error.h> Exception handling framework
Logging <fqtools/logging.h> Logging initialization and level control
Common <fqtools/common/common.h> Timer, IDGenerator, and other utilities

Module Architecture

fq.h (aggregate entry)
  ├── io/          → FastqReader / FastqWriter / FastqRecord / FastqBatch
  ├── processing/  → ProcessingPipelineInterface / Predicate / Mutator
  ├── statistics/  → StatisticCalculatorInterface
  ├── core/        → SequenceUtils
  ├── config/      → Configuration
  ├── error/       → FastQException hierarchy
  ├── logging/     → init / setLevel
  └── common/      → Timer / IDGenerator / Logger

Quick Examples

Statistical Analysis

#include <fqtools/fq.h>

fq::statistic::StatisticOptions options;
options.inputFastqPath = "input.fastq.gz";
options.outputStatPath = "output.stat.txt";

auto calculator = fq::statistic::createStatisticCalculator(options);
calculator->run();

Filtering

#include <fqtools/fq.h>

auto pipeline = fq::processing::createProcessingPipeline();
pipeline->setInputPath("input.fq.gz");
pipeline->setOutputPath("filtered.fq.gz");

fq::processing::ProcessingConfig config;
config.batchSize = 10000;
config.threadCount = 4;
pipeline->setProcessingConfig(config);

// Add filter predicates
pipeline->addReadPredicate(
    std::make_unique<fq::processing::MinQualityPredicate>(20.0, 33));
pipeline->addReadPredicate(
    std::make_unique<fq::processing::MinLengthPredicate>(50));

// Add trimmer
pipeline->addReadMutator(
    std::make_unique<fq::processing::QualityTrimmer>(
        20.0, 50, fq::processing::QualityTrimmer::TrimMode::Both, 33));

auto stats = pipeline->run();
std::cout << stats.toString() << std::endl;

CMake Integration

find_package(FastQTools REQUIRED)
target_link_libraries(my_app PRIVATE FastQTools::FastQTools)

Detailed Documentation