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1 // ***************************************************************************
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2 // BamWriter.cpp (c) 2009 Michael Str�mberg, 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: 22 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 #include <BamWriter.h>
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12 #include <BamWriter_p.h>
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13 using namespace BamTools;
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14 using namespace BamTools::Internal;
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15
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16 #include <iostream>
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17 using namespace std;
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18
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19 // constructor
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20 BamWriter::BamWriter(void) {
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21 d = new BamWriterPrivate;
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22 }
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23
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24 // destructor
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25 BamWriter::~BamWriter(void) {
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26 delete d;
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27 d = 0;
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28 }
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29
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30 // closes the alignment archive
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31 void BamWriter::Close(void) {
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32 d->Close();
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33 }
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34
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35 // opens the alignment archive
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36 bool BamWriter::Open(const string& filename,
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37 const string& samHeader,
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38 const RefVector& referenceSequences,
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39 bool isWriteUncompressed)
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40 {
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41 return d->Open(filename, samHeader, referenceSequences, isWriteUncompressed);
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42 }
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43
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44 // saves the alignment to the alignment archive
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45 void BamWriter::SaveAlignment(const BamAlignment& al) {
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46 d->SaveAlignment(al);
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47 }
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