src/api/BamMultiReader.cpp

   1 // ***************************************************************************
   2 // BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Last modified: 23 December 2010 (DB)
   7 // ---------------------------------------------------------------------------
   8 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
   9 // Institute.
  10 // ---------------------------------------------------------------------------
  11 // Functionality for simultaneously reading multiple BAM files.
  12 //
  13 // This functionality allows applications to work on very large sets of files
  14 // without requiring intermediate merge, sort, and index steps for each file
  15 // subset.  It also improves the performance of our merge system as it
  16 // precludes the need to sort merged files.
  17 // ***************************************************************************
  18
  19 #include <api/BamMultiReader.h>
  20 #include <api/BGZF.h>
  21 #include <api/internal/BamMultiReader_p.h>
  22 using namespace BamTools;
  23
  24 #include <string>
  25 #include <vector>
  26 using namespace std;
  27
  28 // -----------------------------------------------------
  29 // BamMultiReader implementation
  30 // -----------------------------------------------------
  31
  32 BamMultiReader::BamMultiReader(void)
  33     : d(new Internal::BamMultiReaderPrivate)
  34 { }
  35
  36 BamMultiReader::~BamMultiReader(void) {
  37     delete d;
  38     d = 0;
  39 }
  40
  41 void BamMultiReader::Close(void) {
  42     d->Close();
  43 }
  44
  45 bool BamMultiReader::CreateIndexes(bool useStandardIndex) {
  46     return d->CreateIndexes(useStandardIndex);
  47 }
  48
  49 void BamMultiReader::SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode) {
  50     d->SetIndexCacheMode(mode);
  51 }
  52
  53 const string BamMultiReader::GetHeaderText(void) const {
  54     return d->GetHeaderText();
  55 }
  56
  57 bool BamMultiReader::GetNextAlignment(BamAlignment& nextAlignment) {
  58     return d->GetNextAlignment(nextAlignment);
  59 }
  60
  61 bool BamMultiReader::GetNextAlignmentCore(BamAlignment& nextAlignment) {
  62     return d->GetNextAlignmentCore(nextAlignment);
  63 }
  64
  65 const int BamMultiReader::GetReferenceCount(void) const {
  66     return d->GetReferenceCount();
  67 }
  68
  69 const BamTools::RefVector BamMultiReader::GetReferenceData(void) const {
  70     return d->GetReferenceData();
  71 }
  72
  73 const int BamMultiReader::GetReferenceID(const string& refName) const {
  74     return d->GetReferenceID(refName);
  75 }
  76
  77 bool BamMultiReader::HasOpenReaders() {
  78     return d->HasOpenReaders();
  79 }
  80
  81 bool BamMultiReader::IsIndexLoaded(void) const {
  82     return d->IsIndexLoaded();
  83 }
  84
  85 bool BamMultiReader::Jump(int refID, int position) {
  86     return d->Jump(refID, position);
  87 }
  88
  89 bool BamMultiReader::Open(const vector<string>& filenames,
  90                           bool openIndexes,
  91                           bool coreMode,
  92                           bool preferStandardIndex)
  93 {
  94     return d->Open(filenames, openIndexes, coreMode, preferStandardIndex);
  95 }
  96
  97 void BamMultiReader::PrintFilenames(void) const {
  98     d->PrintFilenames();
  99 }
 100
 101 bool BamMultiReader::Rewind(void) {
 102     return d->Rewind();
 103 }
 104
 105 bool BamMultiReader::SetRegion(const int& leftRefID,
 106                                const int& leftPosition,
 107                                const int& rightRefID,
 108                                const int& rightPosition)
 109 {
 110     BamRegion region(leftRefID, leftPosition, rightRefID, rightPosition);
 111     return d->SetRegion(region);
 112 }
 113
 114 bool BamMultiReader::SetRegion(const BamRegion& region) {
 115     return d->SetRegion(region);
 116 }
 117
 118 void BamMultiReader::SetSortOrder(const SortOrder& order) {
 119     d->SetSortOrder(order);
 120 }