/**
** Copyright (c) 2007-2010 Illumina, Inc.
**
** This software is covered by the "Illumina Genome Analyzer Software
** License Agreement" and the "Illumina Source Code License Agreement",
** and certain third party copyright/licenses, and any user of this
** source file is bound by the terms therein (see accompanying files
** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
** Illumina_Source_Code_License_Agreement.pdf and third party
** copyright/license notices).
**
** This file is part of the Consensus Assessment of Sequence And VAriation
** (CASAVA) software package.
**
** @file BamAlignmentReader.h
**
** @brief Provides a wrapper for bam_streamer that fills the Alignment data
**        structure.
**
** @author Michael Stromberg
**/

#pragma once

#include <string>
#include "blt_util/bam_streamer.hh"
#include "common/Alignment.hh"


namespace ca {
namespace variance_detection {

class BamAlignmentReader {
public:
    // constructor
    // if isFilterUnanchored, remove reads where both mates have SE score=0:
    BamAlignmentReader(const bool isFilterUnanchored);
    // destructor
    ~BamAlignmentReader(void);
    // closes the underlying file stream(s)
    void Close(void);
    // provides the next alignment and returns false if no more reads are available
    bool GetNextRead(casava::common::Alignment& al);
    // returns true if the underlying file stream is open
    bool IsOpen(void) const;
    // opens the underlying file stream
    void Open(const std::string& bamFilename, const std::string& refFilename, const char* bamRegion);

private:
    // adds the bases from a bam_seq to an alignment string
    static void AddBases(const bam_seq& br, casava::common::Alignment& al, const bool onForwardStrand);
    // adds the base qualities from an array to an alignment string
    static void AddBaseQualities(const uint8_t* bq, const uint32_t numBases, casava::common::Alignment& al, const bool onForwardStrand);
    // adds the index sequence to an alignment string
    static void AddIndex(const char* indexSeq, casava::common::Alignment& al);
    // adds the read name into machine name, run id, etc.
    static void AddReadName(casava::common::Alignment& al, const char* readName, bool& useCasavaReadNameStyle);
    // returns true if the alignment contains supported CIGAR operations, does not fail QC, and is not a duplicate
    static bool IsGoodAlignment(const bam_record* pBamAlignment, const uint32_t refLen, const bool isFilterUnanchored);
    // toggled according to the status of the underlying file stream(s)
    bool mIsOpen;
    // our underlying input stream
    bam_streamer* mpInStream;
    // the BAM filename
    std::string mFilename;
    // the reference sequence name and bases
    std::string mReferenceBases;
    const char* mpReferenceBases;
    const char* mpReferenceEnd;
    uint32_t mReferenceLen;
    // uses the read name convention used by CASAVA
    bool mUseCasavaReadNameStyle;

    // remove unanchored read pairs
    bool mIsFilterUnanchored;
};

}
}