libpbbam-dev 0.7.4+ds-1 / usr / include / pbbam / internal / ReadGroupInfo.inl

// Copyright (c) 2014-2015, 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 ReadGroupInfo.inl
/// \brief Inline implementations for the ReadGroupInfo class.
//
// Author: Derek Barnett

#include <stdexcept>
#include "pbbam/ReadGroupInfo.h"

namespace PacBio {
namespace BAM {

inline size_t ReadGroupInfo::BarcodeCount(void) const
{
    if (!hasBarcodeData_)
        throw std::runtime_error("barcode count requested but barcode data is missing");
    return barcodeCount_;
}

inline ReadGroupInfo& ReadGroupInfo::BarcodeData(const std::string& barcodeFile,
                                                 const std::string& barcodeHash,
                                                 size_t barcodeCount,
                                                 BarcodeModeType barcodeMode,
                                                 BarcodeQualityType barcodeQuality)
{
    barcodeFile_ = barcodeFile;
    barcodeHash_ = barcodeHash;
    barcodeCount_ = barcodeCount;
    barcodeMode_ = barcodeMode;
    barcodeQuality_ = barcodeQuality;
    hasBarcodeData_ = true;
    return *this;
}

inline std::string ReadGroupInfo::BarcodeFile(void) const
{
    if (!hasBarcodeData_)
        throw std::runtime_error("barcode file requested but barcode data is missing");
    return barcodeFile_;
}

inline std::string ReadGroupInfo::BarcodeHash(void) const
{
    if (!hasBarcodeData_)
        throw std::runtime_error("barcode hash requested but barcode data is missing");
    return barcodeHash_;
}

inline BarcodeModeType ReadGroupInfo::BarcodeMode(void) const
{
    if (!hasBarcodeData_)
        throw std::runtime_error("barcode mode requested but barcode data is missing");
    return barcodeMode_;
}

inline BarcodeQualityType ReadGroupInfo::BarcodeQuality(void) const
{
    if (!hasBarcodeData_)
        throw std::runtime_error("barcode quality requested but barcode data is missing");
    return barcodeQuality_;
}

inline std::string ReadGroupInfo::BasecallerVersion(void) const
{ return basecallerVersion_; }

inline ReadGroupInfo& ReadGroupInfo::BasecallerVersion(const std::string& versionNumber)
{ basecallerVersion_ = versionNumber; return *this; }

inline std::string ReadGroupInfo::BaseFeatureTag(const BaseFeature& feature) const
{
    const auto iter = features_.find(feature);
    if (iter == features_.end())
        return std::string();
    return iter->second;
}

inline ReadGroupInfo& ReadGroupInfo::BaseFeatureTag(const BaseFeature& feature,
                                                    const std::string& tag)
{ features_[feature] = tag; return *this; }

inline std::string ReadGroupInfo::BindingKit(void) const
{ return bindingKit_; }

inline ReadGroupInfo& ReadGroupInfo::BindingKit(const std::string& kitNumber)
{ bindingKit_ = kitNumber; return *this; }

inline ReadGroupInfo& ReadGroupInfo::ClearBarcodeData(void)
{
    barcodeFile_.clear();
    barcodeHash_.clear();
    hasBarcodeData_ = false;
    return *this;
}

inline ReadGroupInfo& ReadGroupInfo::ClearBaseFeatures(void)
{
    features_.clear();
    return *this;
}

inline bool ReadGroupInfo::Control(void) const
{ return control_; }

inline ReadGroupInfo& ReadGroupInfo::Control(const bool ctrl)
{ control_ = ctrl; return *this; }

inline std::map<std::string, std::string> ReadGroupInfo::CustomTags(void) const
{ return custom_; }

inline ReadGroupInfo& ReadGroupInfo::CustomTags(const std::map<std::string, std::string>& custom)
{ custom_ = custom; return *this; }

inline std::string ReadGroupInfo::Date(void) const
{ return date_; }

inline ReadGroupInfo& ReadGroupInfo::Date(const std::string& date)
{ date_ = date; return *this; }

inline std::string ReadGroupInfo::FlowOrder(void) const
{ return flowOrder_; }

inline ReadGroupInfo& ReadGroupInfo::FlowOrder(const std::string& order)
{ flowOrder_ = order; return *this; }

inline std::string ReadGroupInfo::FrameRateHz(void) const
{ return frameRateHz_; }

inline ReadGroupInfo& ReadGroupInfo::FrameRateHz(const std::string& frameRateHz)
{ frameRateHz_ = frameRateHz; return *this; }

inline bool ReadGroupInfo::HasBarcodeData(void) const
{ return hasBarcodeData_; }

inline bool ReadGroupInfo::HasBaseFeature(const BaseFeature& feature) const
{ return features_.find(feature) != features_.end(); }

inline std::string ReadGroupInfo::Id(void) const
{ return id_; }

inline ReadGroupInfo& ReadGroupInfo::Id(const std::string& id)
{ id_ = id; return *this; }

inline ReadGroupInfo& ReadGroupInfo::Id(const std::string& movieName,
                                        const std::string& readType)
{ id_ = MakeReadGroupId(movieName, readType); return *this; }

inline int32_t ReadGroupInfo::IdToInt(const std::string& rgId)
{
    const uint32_t rawid = std::stoul(rgId, nullptr, 16);
    return static_cast<int32_t>(rawid);
}

inline FrameCodec ReadGroupInfo::IpdCodec(void) const
{ return ipdCodec_; }

inline bool ReadGroupInfo::IsValid(void) const
{ return !id_.empty(); }

inline std::string ReadGroupInfo::KeySequence(void) const
{ return keySequence_; }

inline ReadGroupInfo& ReadGroupInfo::KeySequence(const std::string& sequence)
{ keySequence_ = sequence; return *this; }

inline std::string ReadGroupInfo::Library(void) const
{ return library_; }

inline ReadGroupInfo& ReadGroupInfo::Library(const std::string& library)
{ library_ = library; return *this; }

inline std::string ReadGroupInfo::MovieName(void) const
{ return movieName_; }

inline ReadGroupInfo& ReadGroupInfo::MovieName(const std::string& movieName)
{ movieName_ = movieName; return *this; }

inline std::string ReadGroupInfo::Platform(void) const
{ return std::string("PACBIO"); }

inline PlatformModelType ReadGroupInfo::PlatformModel(void) const
{ return platformModel_; }

inline ReadGroupInfo& ReadGroupInfo::PlatformModel(const PlatformModelType& platform)
{ platformModel_ = platform; return *this; }

inline std::string ReadGroupInfo::PredictedInsertSize(void) const
{ return predictedInsertSize_; }

inline ReadGroupInfo& ReadGroupInfo::PredictedInsertSize(const std::string& size)
{ predictedInsertSize_ = size; return *this; }

inline std::string ReadGroupInfo::Programs(void) const
{ return programs_; }

inline ReadGroupInfo& ReadGroupInfo::Programs(const std::string& programs)
{ programs_ = programs; return *this; }

inline FrameCodec ReadGroupInfo::PulseWidthCodec(void) const
{ return pulseWidthCodec_; }

inline std::string ReadGroupInfo::ReadType(void) const
{ return readType_; }

inline ReadGroupInfo& ReadGroupInfo::ReadType(const std::string& type)
{ readType_ = type; return *this; }

inline ReadGroupInfo& ReadGroupInfo::RemoveBaseFeature(const BaseFeature& feature)
{
    auto iter = features_.find(feature);
    if (iter != features_.end())
        features_.erase(iter);
    return *this;
}

inline std::string ReadGroupInfo::Sample(void) const
{ return sample_; }

inline ReadGroupInfo& ReadGroupInfo::Sample(const std::string& sample)
{ sample_ = sample; return *this; }

inline std::string ReadGroupInfo::SequencingCenter(void) const
{ return sequencingCenter_; }

inline ReadGroupInfo& ReadGroupInfo::SequencingCenter(const std::string& center)
{ sequencingCenter_ = center; return *this; }

inline std::string ReadGroupInfo::SequencingChemistry(void) const
{
    return SequencingChemistryFromTriple(BindingKit(),
                                         SequencingKit(),
                                         BasecallerVersion());
}

inline std::string ReadGroupInfo::SequencingKit(void) const
{ return sequencingKit_; }

inline ReadGroupInfo& ReadGroupInfo::SequencingKit(const std::string& kitNumber)
{ sequencingKit_ = kitNumber; return *this; }

inline std::string ReadGroupInfo::ToSam(const ReadGroupInfo& rg)
{ return rg.ToSam(); }

} // namespace BAM
} // namespace PacBio