Bioparser

Bioparser is a c++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

Build

Dependencies

• gcc 4.8+ | clang 3.5+
• zlib 1.2.8+

Hidden

• (bioparser_test) rvaser/biosoup 0.11.0
• (bioparser_test) google/googletest 1.10.0

CMake (3.11+)

git clone https://github.com/rvaser/bioparser && cd bioparser
cmake -B build -DCMAKE_BUILD_TYPE=Release
make -C build

Options

• bioparser_install: generate install target
• bioparser_build_tests: build unit tests

Meson (0.60.0+)

git clone https://github.com/rvaser/bioparser && cd bioparser
meson setup build
ninja -C build

Options

• tests: build unit tests

Examples

FASTA parser

#include "bioparser/fasta_parser.hpp"

struct Sequence {  // or any other name
 public:
  Sequence(  // required arguments
      const char*, std::uint32_t,
      const char*, std::uint32_t) {
    // implementation
  }
}
auto p = bioparser::Parser<Sequence>::Create<bioparser::FastaParser>(path);

// parse whole file
auto s = p->Parse(-1);

FASTQ parser

#include "bioparser/fastq_parser.hpp"

struct Sequence {  // or any other name
 public:
  Sequence(  // required arguments
      const char*, std::uint32_t,
      const char*, std::uint32_t,
      const char*, std::uint32_t) {
    // implementation
  }
}
auto p = bioparser::Parser<Sequence>::Create<bioparser::FastqParser>(path);

// parse in chunks
std::vector<std::unique_ptr<Sequence>> s;
while (true) {
  auto c = p->Parse(1ULL << 30);  // 1 GB
  if (c.empty()) {
    break;
  }
  s.insert(
      s.end(),
      std::make_move_iterator(c.begin()),
      std::make_move_iterator(c.end()));
}

MHAP parser

#include "bioparser/mhap_parser.hpp"

struct Overlap {  // or any other name
 public:
  Overlap(  // required arguments
      std::uint64_t,
      std::uint64_t,
      double error,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t) {
    // implementation
  }
}
auto p = bioparser::Parser<Overlap>::Create<bioparser::MhapParser>(path);

// parse whole file
auto o = p->Parse(-1);

PAF parser

#include "bioparser/paf_parser.hpp"

struct Overlap {  // or any other name
 public:
  Overlap(  // required arguments
      const char*, std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      char,
      const char*, std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      std::uint32_t) {
    // implementation
  }
}
auto p = bioparser::Parser<Overlap>::Create<bioparser::PafParser>(path);

// parse whole file
auto o = p->Parse(-1);

SAM parser

#include "bioparser/sam_parser.hpp"

struct Overlap {  // or any other name
 public:
  Overlap(  // required arguments
      const char*, std::uint32_t,
      std::uint32_t,
      const char*, std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      const char*, std::uint32_t,
      const char*, std::uint32_t,
      std::uint32_t,
      std::uint32_t,
      const char*, std::uint32_t,
      const char*, std::uint32_t) {
    // implementation
  }
}
auto p = bioparser::Parser<Overlap>::Create<bioparser::SamParser>(path);

// parse whole file
auto o = p->Parse(-1);

Note: If your class has a private constructor, add one of the following lines to your class definition:

friend bioparser::FastaParser<Sequence>;
friend bioparser::FastqParser<Sequence>;
friend bioparser::MhapParser<Overlap>;
friend bioparser::PafParser<Overlap>;
friend bioparser::SamParser<Overlap>;

Acknowledgement

This work has been supported in part by the Croatian Science Foundation under the project Single genome and metagenome assembly (IP-2018-01-5886).