/usr/include/pbseq/pbdata/reads/RegionAnnotations.hpp is in libpbdata-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#ifndef _PBDATA_READS_REGION_ANNOTATIONS_HPP_
#define _PBDATA_READS_REGION_ANNOTATIONS_HPP_
#include <algorithm>
#include <string>
#include <vector>
#include "ReadInterval.hpp"
#include "RegionAnnotation.hpp"
class RegionAnnotations {
/// \name Region Annotations of a single ZMW
/// \{
private:
/// \name region table of a zmw
std::vector<RegionAnnotation> table_;
/// \name hole number of a zmw
UInt holeNumber_;
/// \name region types in order.
std::vector<RegionType> types_;
public:
RegionAnnotations(const UInt holeNumber,
const std::vector<RegionAnnotation> & annotations,
const std::vector<RegionType> & types);
RegionAnnotations(const RegionAnnotations & rhs);
~RegionAnnotations() {}
/// \returns zmw holeNumber.
UInt HoleNumber(void) const;
/// \returns sorted adapters of this zmw
std::vector<RegionAnnotation> Adapters() const;
/// \returns whether or not has HQ region specified in table.
bool HasHQRegion() const;
/// \returns exactly one HQ region of this zmw.
/// \note If no HQ region exists, return a RegionAnnotation of length 0.
/// If more than one HQ region is found for this zmw, raise an assertion error.
RegionAnnotation TheHQRegion() const;
/// \returns HQ start position of this zmw.
DNALength HQStart() const;
/// \returns HQ end position of this zmw.
DNALength HQEnd() const;
/// \returns HQ score of this zmw.
int HQScore() const;
/// \returns sorted insert regions of this zmw.
std::vector<RegionAnnotation> Inserts() const;
/// \returns a vector of all adapters
std::vector<ReadInterval> AdapterIntervals() const;
/// \returns a vector of all subreads
/// \param[in] wholeLength Length of unrolled sequence of this zmw. Note that
/// this piece of info does not exist in region table.
/// \param[in] byAdapter false: return inserts in region table directly.
/// true : infer inserts according to adapters.
/// \param[in] byHQRegion false: inserts may contain both HQ and LQ regions
/// true : inserts in HQ regions only.
std::vector<ReadInterval>
SubreadIntervals(const DNALength wholeLength,
const bool byAdapter = true,
const bool byHQRegion = true) const;
private:
/// \returns sorted vector of region annotations of a RegionType.
std::vector<RegionAnnotation>
RegionAnnotationsOfType(RegionType type) const;
/// \returns HQ regions of this zmw.
std::vector<RegionAnnotation> HQRegions() const;
/// \}
};
#endif
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