sequence_sam.h

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#pragma once

#include <zlib/zlib.h>

#include <nvbio/io/sequence/sequence.h>
#include <nvbio/io/sequence/sequence_priv.h>
#include <nvbio/basic/console.h>

namespace nvbio {
namespace io {




// SAM format description: http://samtools.sourceforge.net/SAM1.pdf

enum AlignmentFlags
{
    // SAMtools: template having multiple segments in sequencing
    SAMFlag_MultipleSegments = 0x1,
    // each segment properly aligned according to the aligner
    SAMFlag_AllSegmentsAligned = 0x2,
    // segment unmapped
    SAMFlag_SegmentUnmapped = 0x4,
    // next segment in the template unmapped
    SAMFlag_NextSegmentUnmapped = 0x8,
    // SEQ being reverse complemented
    SAMFlag_ReverseComplemented = 0x10,
    // SEQ of the next segment in the template being reversed
    SAMFlag_NextSegmentReverseComplemented = 0x20,
    // the first segment in the template
    SAMFlag_FirstSegment = 0x40,
    // the last segment in the template
    SAMFlag_LastSegment = 0x80,
    // secondary alignment
    SAMFlag_SecondaryAlignment = 0x100,
    // not passing quality controls
    SAMFlag_FailedQC = 0x200,
    // PCR or optical duplicate
    SAMFlag_Duplicate = 0x400,
};


struct SequenceDataFile_SAM : public SequenceDataFile
{
    enum { LINE_BUFFER_INIT_SIZE = 1024 };

    enum SortOrder
    {
        SortOrder_unknown,
        SortOrder_unsorted,
        SortOrder_queryname,
        SortOrder_coordinate,
    };

    SequenceDataFile_SAM(
        const char*                      read_file_name,
        const SequenceDataFile::Options& options);

    virtual int nextChunk(struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps);

    virtual bool rewind();

    bool init(void);

private:
    bool readLine(void);
    void rewindLine(void);
    bool parseHeaderLine(char *start);
    bool parseReferenceSequenceLine(char *start);

    gzFile  fp;                             
    char*   linebuf;                        
    int     linebuf_size;                   
    int     line_length;                    
    int     numLines;                       

    // info from the header
    char *version;                          
    SortOrder sortOrder;                    

public:
    // reference sequence info
    std::vector<std::string> sq_names;
    std::vector<uint64> sq_lengths;
};

}
}