sam.h

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 * nvbio
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#pragma once

#include <zlib/zlib.h>

#include <nvbio/io/reads/reads.h>
#include <nvbio/io/reads/reads_priv.h>
#include <nvbio/basic/console.h>

namespace nvbio {
namespace io {

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

// flag comments come from SAMtools spec
// a better explanation is available at:
// http://genome.sph.umich.edu/wiki/SAM#What_Information_Does_SAM.2FBAM_Have_for_an_Alignment
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,
};


// ReadDataFile from a SAM file
struct ReadDataFile_SAM : public ReadDataFile
{
    enum { LINE_BUFFER_INIT_SIZE = 1024 };

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

    ReadDataFile_SAM(const char *read_file_name,
                     const uint32 max_reads,
                     const uint32 max_read_len,
                     const ReadEncoding flags);

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

    bool init(void);

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

    gzFile fp;

    // a buffer for a full line; this will grow as needed
    char *linebuf;
    // current size of the buffer
    int linebuf_size;
    // length of the current line in the buffer
    int line_length;

    // how many lines we parsed so far
    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;
};

}
}