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// Copyright (c) 2016, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
//
// File Description
/// \file FastaReader.cpp
/// \brief Implements the FastaReader class.
//
// Author: Derek Barnett
#include "pbbam/FastaReader.h"
#include <htslib/faidx.h>
#include <stdexcept>
#include <fstream>
#include <iostream>
#include <limits>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace std;
namespace PacBio {
namespace BAM {
namespace internal {
struct FastaReaderPrivate
{
ifstream stream_;
string name_;
string bases_;
FastaReaderPrivate(const std::string& fn)
: stream_(fn)
{
if (!stream_)
throw std::runtime_error("FastaReader - could not open " + fn + " for reading");
FetchNext();
}
bool GetNext(FastaSequence& record)
{
if (name_.empty() && bases_.empty())
return false;
record = FastaSequence { name_, bases_ };
FetchNext();
return true;
}
private:
void FetchNext(void)
{
name_.clear();
bases_.clear();
SkipNewlines();
ReadName();
ReadBases();
}
inline void SkipNewlines(void)
{
if (!stream_)
return;
if (stream_.peek() == '\n')
stream_.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
}
void ReadName(void) {
if (!stream_)
return;
if (stream_.get() == '>')
std::getline(stream_, name_, '\n');
}
void ReadBases(void)
{
if (!stream_)
return;
char c = static_cast<char>(stream_.peek());
string line;
while (c != '>') {
if (!stream_)
return;
std::getline(stream_, line, '\n');
bases_ += line;
if (!stream_)
return;
c = static_cast<char>(stream_.peek());
}
}
};
} // namespace internal
} // namespace BAM
} // namespace PacBio
FastaReader::FastaReader(const std::string& fn)
: d_{ new internal::FastaReaderPrivate{ fn } }
{ }
FastaReader::FastaReader(FastaReader&& other)
: d_{ std::move(other.d_) }
{ }
FastaReader& FastaReader::operator=(FastaReader&& other)
{
d_.swap(other.d_);
return *this;
}
FastaReader::~FastaReader(void) { }
bool FastaReader::GetNext(FastaSequence& record)
{ return d_->GetNext(record); }
vector<FastaSequence> FastaReader::ReadAll(const string& fn)
{
vector<FastaSequence> result;
result.reserve(256);
FastaReader reader{ fn };
FastaSequence s;
while(reader.GetNext(s))
result.emplace_back(s);
return result;
}
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