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// Copyright (c) 2020 Robert Vaser
#ifndef BIOPARSER_SAM_PARSER_HPP_
#define BIOPARSER_SAM_PARSER_HPP_
#include <cstdint>
#include <cstdlib>
#include <memory>
#include <vector>
#include <stdexcept>
#include "bioparser/parser.hpp"
namespace bioparser {
template<class T>
class SamParser: public Parser<T> {
public:
SamParser(const SamParser&) = delete;
SamParser& operator=(const SamParser&) = delete;
SamParser(SamParser&&) = delete;
SamParser& operator=(SamParser&&) = delete;
~SamParser() {}
std::vector<std::unique_ptr<T>> Parse(
std::uint64_t bytes, bool shorten_names = true) override {
std::vector<std::unique_ptr<T>> dst;
std::uint64_t parsed_bytes = 0;
const char* q_name = nullptr;
std::uint32_t q_name_len = 0;
std::uint32_t flag = 0;
const char* t_name = nullptr;
std::uint32_t t_name_len = 0;
std::uint32_t t_begin = 0;
std::uint32_t map_quality = 0;
const char* cigar = nullptr;
std::uint32_t cigar_len = 0;
const char* t_next_name = nullptr;
std::uint32_t t_next_name_len = 0;
std::uint32_t t_next_begin = 0;
std::uint32_t template_len = 0;
const char* data = nullptr;
std::uint32_t data_len = 0;
const char* quality = nullptr;
std::uint32_t quality_len = 0;
auto create_T = [&] () -> void {
if (this->storage()[0] == '@') { // file header
this->Clear();
return;
}
auto storage_ptr = this->RightStrip(
this->storage().data(),
this->storage_ptr());
this->Terminate(storage_ptr);
std::uint32_t num_values = 0;
std::uint32_t begin_ptr = 0;
while (true) {
auto end_ptr = begin_ptr;
while (end_ptr < storage_ptr && this->storage()[end_ptr] != '\t') {
++end_ptr;
}
this->Terminate(end_ptr);
switch (num_values) {
case 0:
q_name = this->storage().data() + begin_ptr;
q_name_len = end_ptr - begin_ptr;
break;
case 1: flag = std::atoi(this->storage().data() + begin_ptr); break;
case 2:
t_name = this->storage().data() + begin_ptr;
t_name_len = end_ptr - begin_ptr;
break;
case 3: t_begin = std::atoi(this->storage().data() + begin_ptr); break; // NOLINT
case 4: map_quality = std::atoi(this->storage().data() + begin_ptr); break; // NOLINT
case 5:
cigar = this->storage().data() + begin_ptr;
cigar_len = end_ptr - begin_ptr;
break;
case 6:
t_next_name = this->storage().data() + begin_ptr;
t_next_name_len = end_ptr - begin_ptr;
break;
case 7: t_next_begin = std::atoi(this->storage().data() + begin_ptr); break; // NOLINT
case 8: template_len = std::atoi(this->storage().data() + begin_ptr); break; // NOLINT
case 9:
data = this->storage().data() + begin_ptr;
data_len = end_ptr - begin_ptr;
break;
case 10:
quality = this->storage().data() + begin_ptr;
quality_len = end_ptr - begin_ptr;
break;
default: break;
}
++num_values;
if (end_ptr == storage_ptr || num_values == 11) {
break;
}
begin_ptr = end_ptr + 1;
}
if (num_values != 11) {
throw std::invalid_argument(
"[bioparser::SamParser] error: invalid file format");
}
q_name_len = shorten_names ?
this->Shorten(q_name, q_name_len) :
this->RightStrip(q_name, q_name_len);
t_name_len = shorten_names ?
this->Shorten(t_name, t_name_len) :
this->RightStrip(t_name, t_name_len);
cigar_len = this->RightStrip(cigar, cigar_len);
t_next_name_len = shorten_names ?
this->Shorten(t_next_name, t_next_name_len) :
this->RightStrip(t_next_name, t_next_name_len);
data_len = this->RightStrip(data, data_len);
quality_len = this->RightStrip(quality, quality_len);
if (q_name_len == 0 || t_name_len == 0 || cigar_len == 0 ||
t_next_name_len == 0 || data_len == 0 || quality_len == 0 ||
(data_len > 1 && quality_len > 1 && data_len != quality_len)) {
throw std::invalid_argument(
"[bioparser::SamParser] error: invalid file format");
}
dst.emplace_back(std::unique_ptr<T>(new T(
q_name, q_name_len,
flag,
t_name, t_name_len, t_begin,
map_quality,
cigar, cigar_len,
t_next_name, t_next_name_len, t_next_begin,
template_len,
data, data_len,
quality, quality_len)));
parsed_bytes += this->storage_ptr();
this->Clear();
};
bool is_eof = false;
while (true) {
auto buffer_ptr = this->buffer_ptr();
for (; buffer_ptr < this->buffer_bytes(); ++buffer_ptr) {
auto c = this->buffer()[buffer_ptr];
if (c == '\n') {
this->Store(buffer_ptr - this->buffer_ptr());
create_T();
if (parsed_bytes >= bytes) {
return dst;
}
}
}
if (this->buffer_ptr() < buffer_ptr) {
this->Store(buffer_ptr - this->buffer_ptr());
}
if (is_eof) {
break;
}
is_eof = this->Read();
}
if (this->storage_ptr() != 0) {
create_T();
}
return dst;
}
private:
explicit SamParser(gzFile file)
: Parser<T>(file, 65536) {} // 64 kB
friend Parser<T>;
};
} // namespace bioparser
#endif // BIOPARSER_SAM_PARSER_HPP_
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