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<a href="_bam_multi_reader_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// Marth Lab, Department of Biology, Boston College</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// Last modified: 14 January 2013 (DB)</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// Convenience class for reading multiple BAM files.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> </div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#ifndef BAMMULTIREADER_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define BAMMULTIREADER_H</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "<a class="code" href="api__global_8h.html">api/api_global.h</a>"</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "<a class="code" href="_bam_reader_8h.html">api/BamReader.h</a>"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <map></span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <sstream></span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <utility></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">namespace </span>Internal {</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keyword">class </span>BamMultiReaderPrivate;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> } <span class="comment">// namespace Internal</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_multi_reader.html"> 26</a></span> <span class="keyword">class </span><a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <a class="code" href="class_bam_tools_1_1_bam_multi_reader.html">BamMultiReader</a> {</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="comment">// enums</span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="comment">// possible merge order strategies</span></div><div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2a84e28c1d03be927b219307f33248f89e"> 31</a></span>  <span class="keyword">enum</span> <a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">MergeOrder</a> { RoundRobinMerge = 0</div><div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2a2af00a6dfb052ee8a23319acfd33839b"> 32</a></span>  , MergeByCoordinate</div><div class="line"><a name="l00033"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2a98ab3051854a1357045117cd1a24e835"> 33</a></span>  , MergeByName</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  };</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="comment">// constructor / destructor</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <a class="code" href="class_bam_tools_1_1_bam_multi_reader.html">BamMultiReader</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  ~<a class="code" href="class_bam_tools_1_1_bam_multi_reader.html">BamMultiReader</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="comment">// public interface</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="comment">// BAM file operations</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="comment">// closes all open BAM files</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">bool</span> Close(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="comment">// close only the requested BAM file</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordtype">bool</span> CloseFile(<span class="keyword">const</span> std::string& filename);</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="comment">// returns list of filenames for all open BAM files</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keyword">const</span> std::vector<std::string> Filenames(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="comment">// returns curent merge order strategy</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a> GetMergeOrder(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="comment">// returns true if multireader has any open BAM files</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordtype">bool</span> HasOpenReaders(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="comment">// performs random-access jump within current BAM files</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">bool</span> Jump(<span class="keywordtype">int</span> refID, <span class="keywordtype">int</span> position = 0);</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="comment">// opens BAM files</span></div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordtype">bool</span> Open(<span class="keyword">const</span> std::vector<std::string>& filenames);</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">// opens a single BAM file, adding to any other current BAM files</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordtype">bool</span> OpenFile(<span class="keyword">const</span> std::string& filename);</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="comment">// returns file pointers to beginning of alignments</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordtype">bool</span> Rewind(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="comment">// sets an explicit merge order, regardless of the BAM files' SO header tag</span></div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">bool</span> SetExplicitMergeOrder(<a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamMultiReader::MergeOrder</a> order);</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="comment">// sets the target region of interest</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keywordtype">bool</span> SetRegion(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a>& region);</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="comment">// sets the target region of interest</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordtype">bool</span> SetRegion(<span class="keyword">const</span> <span class="keywordtype">int</span>& leftRefID,</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>& leftPosition,</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>& rightRefID,</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>& rightPosition);</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="comment">// access alignment data</span></div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="comment">// retrieves next available alignment</span></div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">bool</span> GetNextAlignment(<a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>& alignment);</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="comment">// retrieves next available alignment (without populating the alignment's string data fields)</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordtype">bool</span> GetNextAlignmentCore(<a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>& alignment);</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="comment">// access auxiliary data</span></div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="comment">// returns unified SAM header for all files</span></div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> GetHeader(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="comment">// returns unified SAM header text for all files</span></div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  std::string GetHeaderText(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="comment">// returns number of reference sequences</span></div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordtype">int</span> GetReferenceCount(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="comment">// returns all reference sequence entries.</span></div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keyword">const</span> <a class="code" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">BamTools::RefVector</a> GetReferenceData(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="comment">// returns the ID of the reference with this name.</span></div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keywordtype">int</span> GetReferenceID(<span class="keyword">const</span> std::string& refName) <span class="keyword">const</span>;</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="comment">// BAM index operations</span></div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// creates index files for current BAM files</span></div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordtype">bool</span> CreateIndexes(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a>& type = <a class="code" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamIndex::STANDARD</a>);</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">// returns true if all BAM files have index data available</span></div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">bool</span> HasIndexes(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// looks for index files that match current BAM files</span></div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">bool</span> LocateIndexes(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a>& preferredType = <a class="code" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamIndex::STANDARD</a>);</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="comment">// opens index files for current BAM files.</span></div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordtype">bool</span> OpenIndexes(<span class="keyword">const</span> std::vector<std::string>& indexFilenames);</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="comment">// error handling</span></div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="comment">// ----------------------</span></div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// returns a human-readable description of the last error that occurred</span></div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  std::string GetErrorString(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="comment">// private implementation</span></div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  Internal::BamMultiReaderPrivate* d;</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> };</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="preprocessor">#endif // BAMMULTIREADER_H</span></div><div class="ttc" id="class_bam_tools_1_1_bam_alignment_html"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a></div><div class="ttdoc">The main BAM alignment data structure. </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:32</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_index_html_a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430"><div class="ttname"><a href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430">BamTools::BamIndex::STANDARD</a></div><div class="ttdef"><b>Definition:</b> BamIndex.h:41</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html">BamTools::BamRegion</a></div><div class="ttdoc">Represents a sequential genomic region. </div><div class="ttdef"><b>Definition:</b> BamAux.h:88</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_multi_reader_html_abf4e4909508f19cc4f733a48aa7d1ed2"><div class="ttname"><a href="class_bam_tools_1_1_bam_multi_reader.html#abf4e4909508f19cc4f733a48aa7d1ed2">BamTools::BamMultiReader::MergeOrder</a></div><div class="ttdeci">MergeOrder</div><div class="ttdef"><b>Definition:</b> BamMultiReader.h:31</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_index_html_a3bd9db935c5805ab8dea473c2819058a"><div class="ttname"><a href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamTools::BamIndex::IndexType</a></div><div class="ttdeci">IndexType</div><div class="ttdef"><b>Definition:</b> BamIndex.h:40</div></div>
<div class="ttc" id="api__global_8h_html_a5e3652cae8b48c1ad174f0b06bbd06d0"><div class="ttname"><a href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a></div><div class="ttdeci">#define API_EXPORT</div><div class="ttdef"><b>Definition:</b> api_global.h:18</div></div>
<div class="ttc" id="_bam_reader_8h_html"><div class="ttname"><a href="_bam_reader_8h.html">BamReader.h</a></div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html">BamTools::SamHeader</a></div><div class="ttdoc">Represents the SAM-formatted text header that is part of the BAM file header. </div><div class="ttdef"><b>Definition:</b> SamHeader.h:24</div></div>
<div class="ttc" id="namespace_bam_tools_html"><div class="ttname"><a href="namespace_bam_tools.html">BamTools</a></div><div class="ttdoc">Contains all BamTools classes & methods. </div><div class="ttdef"><b>Definition:</b> Sort.h:24</div></div>
<div class="ttc" id="namespace_bam_tools_html_abf3564b867a24092bf6575fdda87d573"><div class="ttname"><a href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">BamTools::RefVector</a></div><div class="ttdeci">std::vector< RefData > RefVector</div><div class="ttdoc">convenience typedef for vector of RefData entries </div><div class="ttdef"><b>Definition:</b> BamAux.h:74</div></div>
<div class="ttc" id="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_multi_reader_html"><div class="ttname"><a href="class_bam_tools_1_1_bam_multi_reader.html">BamTools::BamMultiReader</a></div><div class="ttdoc">Convenience class for reading multiple BAM files. </div><div class="ttdef"><b>Definition:</b> BamMultiReader.h:26</div></div>
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