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1 // ***************************************************************************
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2 // BamWriter_p.h (c) 2010 Derek Barnett
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3 // Marth Lab, Department of Biology, Boston College
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4 // All rights reserved.
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5 // ---------------------------------------------------------------------------
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6 // Last modified: 19 November 2010 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Provides the basic functionality for producing BAM files
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9 // ***************************************************************************
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10
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11 #ifndef BAMWRITER_P_H
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12 #define BAMWRITER_P_H
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13
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14 // -------------
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15 // W A R N I N G
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16 // -------------
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17 //
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18 // This file is not part of the BamTools API. It exists purely as an
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19 // implementation detail. This header file may change from version to
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20 // version without notice, or even be removed.
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21 //
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22 // We mean it.
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23
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24 #include <BamAux.h>
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25 #include <BGZF.h>
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26 #include <string>
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27 #include <vector>
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28
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29 namespace BamTools {
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30 namespace Internal {
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31
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32 class BamWriterPrivate {
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33
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34 // ctor & dtor
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35 public:
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36 BamWriterPrivate(void);
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37 ~BamWriterPrivate(void);
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38
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39 // "public" interface to BamWriter
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40 public:
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41 void Close(void);
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42 bool Open(const std::string& filename,
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43 const std::string& samHeader,
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44 const BamTools::RefVector& referenceSequences,
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45 bool isWriteUncompressed);
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46 void SaveAlignment(const BamAlignment& al);
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47
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48 // internal methods
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49 public:
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50 const unsigned int CalculateMinimumBin(const int begin, int end) const;
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51 void CreatePackedCigar(const std::vector<BamTools::CigarOp>& cigarOperations, std::string& packedCigar);
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52 void EncodeQuerySequence(const std::string& query, std::string& encodedQuery);
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53
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54 // data members
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55 public:
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56 BgzfData mBGZF;
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57 bool IsBigEndian;
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58 };
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59
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60 } // namespace Internal
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61 } // namespace BamTools
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62
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63 #endif // BAMWRITER_P_H
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