/usr/include/pbbam/internal/CompositeBamReader.inl is in libpbbam-dev 0.7.4+ds-1.
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//
// All rights reserved.
//
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// 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
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// 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 CompositeBamReader.inl
/// \brief Inline implementations for the composite BAM readers, for
/// working with multiple input files.
//
// Author: Derek Barnett
#include "pbbam/CompositeBamReader.h"
#include <algorithm>
#include <set>
#include <sstream>
#include <stdexcept>
namespace PacBio {
namespace BAM {
namespace internal {
// -----------------------------------
// Merging helpers
// -----------------------------------
inline CompositeMergeItem::CompositeMergeItem(std::unique_ptr<BamReader>&& rdr)
: reader(std::move(rdr))
{ }
inline CompositeMergeItem::CompositeMergeItem(std::unique_ptr<BamReader>&& rdr,
BamRecord&& rec)
: reader(std::move(rdr))
, record(std::move(rec))
{ }
inline CompositeMergeItem::CompositeMergeItem(CompositeMergeItem&& other)
: reader(std::move(other.reader))
, record(std::move(other.record))
{ }
inline CompositeMergeItem& CompositeMergeItem::operator=(CompositeMergeItem&& other)
{
reader = std::move(other.reader);
record = std::move(other.record);
return *this;
}
inline CompositeMergeItem::~CompositeMergeItem(void) { }
template<typename CompareType>
inline bool CompositeMergeItemSorter<CompareType>::operator()(const CompositeMergeItem& lhs,
const CompositeMergeItem& rhs)
{
const BamRecord& l = lhs.record;
const BamRecord& r = rhs.record;
return CompareType()(l, r);
}
} // namespace internal
// -----------------------------------
// GenomicIntervalCompositeBamReader
// -----------------------------------
inline GenomicIntervalCompositeBamReader::GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
const std::vector<BamFile>& bamFiles)
{
filenames_.reserve(bamFiles.size());
for(const auto& bamFile : bamFiles)
filenames_.push_back(bamFile.Filename());
Interval(interval);
}
inline GenomicIntervalCompositeBamReader::GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
std::vector<BamFile>&& bamFiles)
{
filenames_.reserve(bamFiles.size());
for(auto&& bamFile : bamFiles)
filenames_.push_back(bamFile.Filename());
Interval(interval);
}
inline GenomicIntervalCompositeBamReader::GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
const DataSet& dataset)
: GenomicIntervalCompositeBamReader(interval, dataset.BamFiles())
{ }
inline bool GenomicIntervalCompositeBamReader::GetNext(BamRecord& record)
{
// nothing left to read
if (mergeItems_.empty())
return false;
// non-destructive 'pop' of first item from queue
auto firstIter = mergeItems_.begin();
auto firstItem = internal::CompositeMergeItem{ std::move(firstIter->reader), std::move(firstIter->record) };
mergeItems_.pop_front();
// store its record in our output record
std::swap(record, firstItem.record);
// try fetch 'next' from first item's reader
// if successful, re-insert it into container & re-sort on our new values
// otherwise, this item will go out of scope & reader destroyed
if (firstItem.reader->GetNext(firstItem.record)) {
mergeItems_.push_front(std::move(firstItem));
UpdateSort();
}
// return success
return true;
}
inline const GenomicInterval& GenomicIntervalCompositeBamReader::Interval(void) const
{ return interval_; }
inline GenomicIntervalCompositeBamReader& GenomicIntervalCompositeBamReader::Interval(const GenomicInterval& interval)
{
auto updatedMergeItems = std::deque<internal::CompositeMergeItem>{ };
auto filesToCreate = std::set<std::string>{ filenames_.cbegin(), filenames_.cend() };
// update existing readers
while (!mergeItems_.empty()) {
// non-destructive 'pop' of first item from queue
auto firstIter = mergeItems_.begin();
auto firstItem = internal::CompositeMergeItem{ std::move(firstIter->reader), std::move(firstIter->record) };
mergeItems_.pop_front();
// reset interval
BaiIndexedBamReader* baiReader = dynamic_cast<BaiIndexedBamReader*>(firstItem.reader.get());
assert(baiReader);
baiReader->Interval(interval);
// try fetch 'next' from first item's reader
// if successful, re-insert it into container & re-sort on our new values
// otherwise, this item will go out of scope & reader destroyed
if (firstItem.reader->GetNext(firstItem.record)) {
updatedMergeItems.push_front(std::move(firstItem));
filesToCreate.erase(firstItem.reader->Filename());
}
}
// create readers for files that were not 'active' for the previous
std::vector<std::string> missingBai;
for (auto&& fn : filesToCreate) {
auto bamFile = BamFile{ fn };
if (bamFile.StandardIndexExists()) {
auto item = internal::CompositeMergeItem{ std::unique_ptr<BamReader>{ new BaiIndexedBamReader{ interval, std::move(bamFile) } } };
if (item.reader->GetNext(item.record))
updatedMergeItems.push_back(std::move(item));
// else not an error, simply no data matching interval
}
else {
// maybe handle PBI-backed interval searches if BAI missing, but for now treat as error
missingBai.push_back(bamFile.Filename());
}
}
// throw if any files missing BAI
if (!missingBai.empty()) {
std::stringstream e;
e << "failed to open GenomicIntervalCompositeBamReader because the following files are missing a BAI file:" << std::endl;
for (const auto& fn : missingBai)
e << " " << fn << std::endl;
throw std::runtime_error(e.str());
}
// update our actual container and return
mergeItems_ = std::move(updatedMergeItems);
UpdateSort();
return *this;
}
struct OrderByPosition
{
static inline bool less_than(const BamRecord& lhs, const BamRecord& rhs)
{
const int32_t lhsId = lhs.ReferenceId();
const int32_t rhsId = rhs.ReferenceId();
if (lhsId == -1) return false;
if (rhsId == -1) return true;
if (lhsId == rhsId)
return lhs.ReferenceStart() < rhs.ReferenceStart();
else return lhsId < rhsId;
}
static inline bool equals(const BamRecord& lhs, const BamRecord& rhs)
{
return lhs.ReferenceId() == rhs.ReferenceId() &&
lhs.ReferenceStart() == rhs.ReferenceStart();
}
};
struct PositionSorter : std::binary_function<internal::CompositeMergeItem, internal::CompositeMergeItem, bool>
{
bool operator()(const internal::CompositeMergeItem& lhs,
const internal::CompositeMergeItem& rhs)
{
const BamRecord& l = lhs.record;
const BamRecord& r = rhs.record;
return OrderByPosition::less_than(l, r);
}
};
inline void GenomicIntervalCompositeBamReader::UpdateSort(void)
{ std::sort(mergeItems_.begin(), mergeItems_.end(), PositionSorter{ }); }
// ------------------------------
// PbiRequestCompositeBamReader
// ------------------------------
template<typename OrderByType>
inline PbiFilterCompositeBamReader<OrderByType>::PbiFilterCompositeBamReader(const PbiFilter& filter,
const std::vector<BamFile>& bamFiles)
{
filenames_.reserve(bamFiles.size());
for(const auto& bamFile : bamFiles)
filenames_.push_back(bamFile.Filename());
Filter(filter);
}
template<typename OrderByType>
inline PbiFilterCompositeBamReader<OrderByType>::PbiFilterCompositeBamReader(const PbiFilter& filter,
std::vector<BamFile>&& bamFiles)
{
filenames_.reserve(bamFiles.size());
for(auto&& bamFile : bamFiles)
filenames_.push_back(bamFile.Filename());
Filter(filter);
}
template<typename OrderByType>
inline PbiFilterCompositeBamReader<OrderByType>::PbiFilterCompositeBamReader(const PbiFilter& filter,
const DataSet& dataset)
: PbiFilterCompositeBamReader(filter, std::move(dataset.BamFiles()))
{ }
template<typename OrderByType>
inline bool PbiFilterCompositeBamReader<OrderByType>::GetNext(BamRecord& record)
{
// nothing left to read
if (mergeQueue_.empty())
return false;
// non-destructive 'pop' of first item from queue
auto firstIter = mergeQueue_.begin();
auto firstItem = value_type{ std::move(firstIter->reader), std::move(firstIter->record) };
mergeQueue_.pop_front();
// store its record in our output record
std::swap(record, firstItem.record);
// try fetch 'next' from first item's reader
// if successful, re-insert it into container & re-sort on our new values
// otherwise, this item will go out of scope & reader destroyed
if (firstItem.reader->GetNext(firstItem.record)) {
mergeQueue_.push_front(std::move(firstItem));
UpdateSort();
}
// return success
return true;
}
template<typename OrderByType>
inline PbiFilterCompositeBamReader<OrderByType>&
PbiFilterCompositeBamReader<OrderByType>::Filter(const PbiFilter& filter)
{
auto updatedMergeItems = container_type{ };
auto filesToCreate = std::set<std::string>{ filenames_.cbegin(), filenames_.cend() };
// update existing readers
while (!mergeQueue_.empty()) {
// non-destructive 'pop' of first item from queue
auto firstIter = mergeQueue_.begin();
auto firstItem = internal::CompositeMergeItem{ std::move(firstIter->reader), std::move(firstIter->record) };
mergeQueue_.pop_front();
// reset request
PbiIndexedBamReader* pbiReader = dynamic_cast<PbiIndexedBamReader*>(firstItem.reader.get());
assert(pbiReader);
pbiReader->Filter(filter);
// try fetch 'next' from first item's reader
// if successful, re-insert it into container & re-sort on our new values
// otherwise, this item will go out of scope & reader destroyed
if (firstItem.reader->GetNext(firstItem.record)) {
updatedMergeItems.push_front(std::move(firstItem));
filesToCreate.erase(firstItem.reader->Filename());
}
}
// create readers for files that were not 'active' for the previous
std::vector<std::string> missingPbi;
for (auto&& fn : filesToCreate) {
auto bamFile = BamFile{ fn };
if (bamFile.PacBioIndexExists()) {
auto item = internal::CompositeMergeItem{ std::unique_ptr<BamReader>{ new PbiIndexedBamReader{ filter, std::move(bamFile) } } };
if (item.reader->GetNext(item.record))
updatedMergeItems.push_back(std::move(item));
// else not an error, simply no data matching filter
}
else
missingPbi.push_back(fn);
}
// throw if any files missing PBI
if (!missingPbi.empty()) {
std::stringstream e;
e << "failed to open PbiFilterCompositeBamReader because the following files are missing a PBI file:" << std::endl;
for (const auto& fn : missingPbi)
e << " " << fn << std::endl;
throw std::runtime_error(e.str());
}
// update our actual container and return
mergeQueue_ = std::move(updatedMergeItems);
UpdateSort();
return *this;
}
template<typename OrderByType>
inline void PbiFilterCompositeBamReader<OrderByType>::UpdateSort(void)
{ std::stable_sort(mergeQueue_.begin(), mergeQueue_.end(), merge_sorter_type{}); }
// ------------------------------
// SequentialCompositeBamReader
// ------------------------------
inline SequentialCompositeBamReader::SequentialCompositeBamReader(const std::vector<BamFile>& bamFiles)
{
for (auto&& bamFile : bamFiles)
readers_.emplace_back(new BamReader{ bamFile });
}
inline SequentialCompositeBamReader::SequentialCompositeBamReader(std::vector<BamFile>&& bamFiles)
{
for (auto&& bamFile : bamFiles)
readers_.emplace_back(new BamReader{ std::move(bamFile) });
}
inline SequentialCompositeBamReader::SequentialCompositeBamReader(const DataSet& dataset)
: SequentialCompositeBamReader(dataset.BamFiles())
{ }
inline bool SequentialCompositeBamReader::GetNext(BamRecord& record)
{
// try first reader, if successful return true
// else pop reader and try next, until all readers exhausted
while (!readers_.empty()) {
auto& reader = readers_.front();
if (reader->GetNext(record))
return true;
else
readers_.pop_front();
}
// no readers available
return false;
}
} // namespace BAM
} // namespace PacBio
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