/usr/include/pbbam/virtual/VirtualRegion.h is in libpbbam-dev 0.7.4+ds-1.
This file is owned by root:root, with mode 0o644.
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// 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.
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// * 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.
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// from this software without specific prior written permission.
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// SUCH DAMAGE.
//
// File Description
/// \file VirtualRegion.h
/// \brief Defines the VirtualRegion class.
//
// Author: Armin Töpfer
#ifndef VIRTUALREGION_H
#define VIRTUALREGION_H
#include "pbbam/Config.h"
#include "pbbam/virtual/VirtualRegionType.h"
#include "pbbam/LocalContextFlags.h"
namespace PacBio {
namespace BAM {
/// \brief The VirtualRegion represents an annotation of a polymerase region.
///
struct VirtualRegion
{
public:
VirtualRegionType type;
int beginPos;
int endPos;
LocalContextFlags cxTag = LocalContextFlags::NO_LOCAL_CONTEXT;
int barcodeLeft = -1;
int barcodeRight = -1;
int score = 0;
public:
/// \brief Creates a virtual region with basic type & position info.
///
VirtualRegion(const VirtualRegionType type,
const int beginPos,
const int endPos,
const int score = 0);
/// \brief Creates a virtual region with type/position info, as well as context & barcode.
///
VirtualRegion(const VirtualRegionType type,
const int beginPos,
const int endPos,
const LocalContextFlags cxTag,
const int barcodeLeft,
const int barcodeRight,
const int score = 0);
VirtualRegion(void) = default;
VirtualRegion(const VirtualRegion&) = default;
VirtualRegion(VirtualRegion&&) = default;
VirtualRegion& operator=(const VirtualRegion&) = default; // un-"delete"-ed for SWIG
VirtualRegion& operator=(VirtualRegion&&) = default;
~VirtualRegion(void) = default;
bool operator==(const VirtualRegion &v1) const;
};
inline VirtualRegion::VirtualRegion(const VirtualRegionType type,
const int beginPos,
const int endPos,
const int score)
: type(type)
, beginPos(beginPos)
, endPos(endPos), cxTag()
, score(score)
{}
inline VirtualRegion::VirtualRegion(const VirtualRegionType type,
const int beginPos,
const int endPos,
const LocalContextFlags cxTag,
const int barcodeLeft,
const int barcodeRight,
const int score)
: type(type)
, beginPos(beginPos)
, endPos(endPos)
, cxTag(cxTag)
, barcodeLeft(barcodeLeft)
, barcodeRight(barcodeRight)
, score(score)
{}
inline bool VirtualRegion::operator==(const VirtualRegion& v1) const
{
return (v1.type == this->type &&
v1.beginPos == this->beginPos &&
v1.endPos == this->endPos);
}
} // namespace BAM
} // namespace PacBio
#endif // VIRTUALREGION_H
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