/usr/include/pbbam/AlignmentPrinter.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
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// * Redistributions in binary form must reproduce the above
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// with the distribution.
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// File Description
/// \file AlignmentPrinter.h
/// \brief Defines the AlignmentPrinter class.
//
// Author: Armin Töpfer
#ifndef ALIGNMENTPRINTER_H
#define ALIGNMENTPRINTER_H
#include <memory>
#include <string>
#include "pbbam/BamRecord.h"
#include "pbbam/IndexedFastaReader.h"
#include "pbbam/Orientation.h"
namespace PacBio {
namespace BAM {
class BamRecord;
/// \brief The AlignmentPrinter class "pretty-prints" an alignment with respect
/// to its associated reference sequence.
///
/// Example output:
/// \verbinclude plaintext/AlignmentPrinterOutput.txt
///
class AlignmentPrinter
{
public:
/// \name Constructors & Related Methods
/// \{
/// Constructs the alignment printer with an associated FASTA file reader.
///
/// \param[in] ifr FASTA reader
///
/// \throws std::runtime_error if FASTA file cannot be opened for reading.
///
AlignmentPrinter(const IndexedFastaReader& ifr);
AlignmentPrinter(void) = delete;
AlignmentPrinter(const AlignmentPrinter&) = delete;
AlignmentPrinter(AlignmentPrinter&&) = default;
AlignmentPrinter& operator=(const AlignmentPrinter&) = delete;
AlignmentPrinter& operator=(AlignmentPrinter&&) = default;
~AlignmentPrinter(void) = default;
/// \}
public:
/// \name Printing
/// \{
/// Pretty-prints an aligned BamRecord to std::string.
///
/// \note The current implementation includes ANSI escape sequences for
/// coloring terminal output. Future versions of this method will
/// likely make this optional.
///
/// \returns formatted string containing the alignment and summary
/// information
///
std::string Print(const BamRecord& record,
const Orientation orientation = Orientation::GENOMIC);
/// \}
private:
const std::unique_ptr<IndexedFastaReader> ifr_;
};
} // namespace BAM
} // namespace PacBio
#endif // ALIGNMENTPRINTER_H
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