/usr/include/fast5.hpp is in libfast5-dev 0~20150918-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define __FAST5_HPP
#include <cassert>
#include <exception>
#include <iostream>
#include <sstream>
#include <iomanip>
#include <string>
#include <vector>
#include <fast5/hdf5_tools.hpp>
#define MAX_K_LEN 8
namespace fast5
{
//
// This struct represents the expected signal measured
// given the kmer sequence that is in the pore when the
// the observations are made. A pore model consists
// of 1024 of these entries (one per 5-mer) and global
// shift/scaling parameters.
//
struct Model_Entry
{
char kmer[MAX_K_LEN];
long long variant;
double level_mean;
double level_stdv;
double sd_mean;
double sd_stdv;
double weight;
}; // struct Model_Entry
//
// This struct represents the global transformations
// that must be applied to each Model_Entry
//
struct Model_Parameters
{
double drift;
double scale;
double scale_sd;
double shift;
double var;
double var_sd;
}; // struct Model_Parameters
//
// This struct represents an observed event.
// The members of the struct are the same as
// the fields encoded in the FAST5 file.
//
struct Event_Entry
{
double mean;
double start;
double stdv;
double length;
char model_state[MAX_K_LEN];
double model_level;
long long move;
double p_model_state;
char mp_state[MAX_K_LEN];
double p_mp_state;
double p_A;
double p_C;
double p_G;
double p_T;
}; // struct Event_Entry
//
// This struct represents a template-to-complement
// match that is emitted by ONT's 2D basecaller
//
struct Event_Alignment_Entry
{
long long template_index;
long long complement_index;
char kmer[MAX_K_LEN];
}; // struct Event_Alignment_Entry
class File
: private hdf5_tools::File_Reader
{
private:
typedef hdf5_tools::File_Reader Base;
public:
using Base::Base;
using Base::is_open;
using Base::file_name;
using Base::open;
using Base::close;
std::string file_version() const
{
double v;
assert(Base::exists("/file_version"));
Base::read< double >("/file_version", v);
// convert it to string
std::ostringstream os;
os << v;
return os.str();
}
std::string basecall_version() const
{
std::string res;
std::string path = get_bc_2d_root() + "/version";
assert(Base::exists(path));
Base::read< std::string >(path, res);
return res;
}
std::string eventdetection_version() const
{
std::string res;
// only support eventdetection group 000 for now
std::string path = "/Analyses/EventDetection_000/version";
assert(Base::exists(path));
Base::read< std::string >(path, res);
return res;
}
std::string get_log() const
{
std::string res;
std::string path = get_bc_2d_root() + "/Log";
assert(Base::exists(path));
Base::read< std::string >(path, res);
return res;
}
double get_sampling_rate() const
{
assert(have_sampling_rate());
auto lg = get_log();
auto idx = lg.find("Sampling rate is");
std::string line;
std::stringstream ss1(lg.substr(idx));
std::getline(ss1,line,'\n');
std::stringstream ss2(line);
std::string token;
std::getline(ss2,token,' '); //Sampling
std::getline(ss2,token,' '); //rate
std::getline(ss2,token,' '); //is
std::getline(ss2,token,' '); //Hz value
return std::atof(token.c_str());
}
bool have_sampling_rate() const
{
auto lg = get_log();
auto idx = lg.find("Sampling rate is");
return idx != std::string::npos;
}
std::string get_model_file(size_t i) const
{
std::string res;
assert(Base::exists(model_file_path(i)));
Base::read< std::string >(model_file_path(i), res);
return res;
}
std::string sequences_version() const
{
std::vector< std::string > tmp;
assert(Base::exists("/Sequences/Meta/version"));
Base::read< std::string >("/Sequences/Meta/version", tmp);
std::string res;
for (const auto& s: tmp)
{
res += s;
}
return res;
}
bool have_basecalled_2D() const
{
return Base::exists(get_bc_2d_root() + "/BaseCalled_2D/Fastq");
}
std::string basecalled_2D() const
{
std::string res;
Base::read< std::string >(get_bc_2d_root() + "/BaseCalled_2D/Fastq", res);
// Split the FASTQ record on newlines
size_t nl1 = res.find_first_of('\n');
size_t nl2 = res.find_first_of('\n', nl1 + 1);
if(nl1 == std::string::npos || nl2 == std::string::npos)
return "";
else
return res.substr(nl1 + 1, nl2 - nl1 - 1);
}
std::vector< Event_Alignment_Entry > get_event_alignments() const
{
std::vector< Event_Alignment_Entry > res;
hdf5_tools::Compound_Map m;
m.add_member("template", &Event_Alignment_Entry::template_index);
m.add_member("complement", &Event_Alignment_Entry::complement_index);
m.add_member("kmer", &Event_Alignment_Entry::kmer);
Base::read< Event_Alignment_Entry >(get_bc_2d_root() + "/BaseCalled_2D/Alignment", res, &m);
return res;
}
bool have_model(size_t i) const
{
return Base::exists(model_path(i));
}
bool have_events(size_t i) const
{
return Base::exists(events_path(i));
}
std::vector< Model_Entry > get_model(size_t i) const
{
std::vector< Model_Entry > res;
hdf5_tools::Compound_Map m;
m.add_member("kmer", &Model_Entry::kmer);
m.add_member("level_mean", &Model_Entry::level_mean);
m.add_member("level_stdv", &Model_Entry::level_stdv);
m.add_member("sd_mean", &Model_Entry::sd_mean);
m.add_member("sd_stdv", &Model_Entry::sd_stdv);
Base::read< Model_Entry >(model_path(i), res, &m);
return res;
}
Model_Parameters get_model_parameters(size_t i) const
{
Model_Parameters res;
std::string path = model_path(i);
Base::read< double >(path + "/drift", res.drift);
Base::read< double >(path + "/scale", res.scale);
Base::read< double >(path + "/scale_sd", res.scale_sd);
Base::read< double >(path + "/shift", res.shift);
Base::read< double >(path + "/var", res.var);
Base::read< double >(path + "/var_sd", res.var_sd);
return res;
}
std::vector< Event_Entry > get_events(size_t i) const
{
std::vector< Event_Entry > res;
hdf5_tools::Compound_Map m;
m.add_member("mean", &Event_Entry::mean);
m.add_member("start", &Event_Entry::start);
m.add_member("stdv", &Event_Entry::stdv);
m.add_member("length", &Event_Entry::length);
Base::read< Event_Entry >(events_path(i), res, &m);
return res;
}
void set_basecalled_group_id(size_t i)
{
assert(i <= 999);
std::stringstream ss;
ss << std::setfill('0') << std::setw(3) << i;
_basecalled_group_id = ss.str();
}
private:
// Returns the root path of the form:
// Analyses/Basecall_2D_ddd/ where ddd is the group
std::string get_bc_2d_root() const
{
return "/Analyses/Basecall_2D_" + _basecalled_group_id;
}
std::string model_path(size_t i) const
{
static std::vector< std::string > _model_path =
{ "/BaseCalled_template/Model",
"/BaseCalled_complement/Model" };
return get_bc_2d_root() + _model_path.at(i);
}
std::string events_path(size_t i) const
{
static std::vector< std::string > _events_path =
{ "/BaseCalled_template/Events",
"/BaseCalled_complement/Events" };
return get_bc_2d_root() + _events_path.at(i);
}
std::string model_file_path(size_t i) const
{
static std::vector< std::string > _model_file_path =
{ "/Summary/basecall_1d_template/model_file",
"/Summary/basecall_1d_complement/model_file" };
return get_bc_2d_root() + _model_file_path.at(i);
}
// default to using the 000 analysis group
std::string _basecalled_group_id = "000";
}; // class File
} // namespace fast5
#endif
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