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1 // ***************************************************************************
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2 // BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg
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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 reading BAM files
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9 // ***************************************************************************
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10
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11 #include <BamReader.h>
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12 #include <BamReader_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 <algorithm>
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17 #include <iostream>
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18 #include <iterator>
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19 #include <string>
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20 #include <vector>
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21 using namespace std;
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22
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23 // constructor
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24 BamReader::BamReader(void) {
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25 d = new BamReaderPrivate(this);
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26 }
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27
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28 // destructor
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29 BamReader::~BamReader(void) {
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30 delete d;
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31 d = 0;
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32 }
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33
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34 // file operations
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35 void BamReader::Close(void) { d->Close(); }
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36 bool BamReader::HasIndex(void) const { return d->HasIndex; }
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37 bool BamReader::IsIndexLoaded(void) const { return HasIndex(); }
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38 bool BamReader::IsOpen(void) const { return d->mBGZF.IsOpen; }
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39 bool BamReader::Jump(int refID, int position) { return d->SetRegion( BamRegion(refID, position) ); }
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40 bool BamReader::Open(const std::string& filename,
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41 const std::string& indexFilename,
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42 const bool lookForIndex,
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43 const bool preferStandardIndex)
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44 {
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45 return d->Open(filename, indexFilename, lookForIndex, preferStandardIndex);
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46 }
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47 bool BamReader::Rewind(void) { return d->Rewind(); }
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48 bool BamReader::SetRegion(const BamRegion& region) { return d->SetRegion(region); }
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49 bool BamReader::SetRegion(const int& leftRefID, const int& leftBound, const int& rightRefID, const int& rightBound) {
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50 return d->SetRegion( BamRegion(leftRefID, leftBound, rightRefID, rightBound) );
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51 }
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52
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53 // access alignment data
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54 bool BamReader::GetNextAlignment(BamAlignment& bAlignment) { return d->GetNextAlignment(bAlignment); }
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55 bool BamReader::GetNextAlignmentCore(BamAlignment& bAlignment) { return d->GetNextAlignmentCore(bAlignment); }
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56
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57 // access auxiliary data
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58 const string BamReader::GetHeaderText(void) const { return d->GetHeaderText(); }
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59 int BamReader::GetReferenceCount(void) const { return d->References.size(); }
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60 const RefVector& BamReader::GetReferenceData(void) const { return d->References; }
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61 int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); }
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62 const std::string BamReader::GetFilename(void) const { return d->Filename; }
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63
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64 // index operations
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65 bool BamReader::CreateIndex(bool useStandardIndex) { return d->CreateIndex(useStandardIndex); }
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66 void BamReader::SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode) { d->SetIndexCacheMode(mode); }
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