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<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_da61e3e9a357748887e3ca8d7c5a0c16.html">api</a></li> </ul>
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<a href="_bam_index_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">// BamIndex.h (c) 2009 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: 10 October 2011 (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">// Provides basic BAM index interface</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 BAM_INDEX_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define BAM_INDEX_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_aux_8h.html">api/BamAux.h</a>"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span>Internal {</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  <span class="keyword">class </span>BamReaderPrivate;</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> } <span class="comment">// namespace Internal</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div><div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_index.html"> 34</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_index.html">BamIndex</a> {</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">// enums</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> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="comment">// list of supported BamIndex types</span></div><div class="line"><a name="l00040"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a"> 40</a></span>  <span class="keyword">enum</span> <a class="code" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">IndexType</a> { BAMTOOLS = 0</div><div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058aa15b7d8aa9dcd545307455ba5115af430"> 41</a></span>  , STANDARD</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</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">// ctor & dtor</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00046"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_index.html#add9e57706ae2057b0e2ee39c5953c073"> 46</a></span>  <a class="code" href="class_bam_tools_1_1_bam_index.html#add9e57706ae2057b0e2ee39c5953c073">BamIndex</a>(Internal::BamReaderPrivate* reader) : m_reader(reader) { }</div><div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_index.html#a891299c6f89d3c7d1da5286e612f9a96"> 47</a></span>  <span class="keyword">virtual</span> <a class="code" href="class_bam_tools_1_1_bam_index.html#a891299c6f89d3c7d1da5286e612f9a96">~BamIndex</a>(<span class="keywordtype">void</span>) { }</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  </div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="comment">// index interface</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="comment">// builds index from associated BAM file & writes out to index file</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> Create(<span class="keywordtype">void</span>) =0;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="comment">// returns a human-readable description of the last error encountered</span></div><div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_index.html#a8e3594d367918d5ed1187f950868f66c"> 55</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_index.html#a8e3594d367918d5ed1187f950868f66c">GetErrorString</a>(<span class="keywordtype">void</span>) { <span class="keywordflow">return</span> m_errorString; }</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="comment">// returns whether reference has alignments or no</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> HasAlignments(<span class="keyword">const</span> <span class="keywordtype">int</span>& referenceID) <span class="keyword">const</span> =0;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="comment">// attempts to use index data to jump to @region, returns success/fail</span></div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="comment">// a "successful" jump indicates no error, but not whether this region has data</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">// * thus, the method sets a flag to indicate whether there are alignments</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="comment">// available after the jump position</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> Jump(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html">BamTools::BamRegion</a>& region, <span class="keywordtype">bool</span>* hasAlignmentsInRegion) =0;</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="comment">// loads existing data from file into memory</span></div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> Load(<span class="keyword">const</span> std::string& filename) =0;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="comment">// returns the 'type' enum for derived index format</span></div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keyword">virtual</span> <a class="code" href="class_bam_tools_1_1_bam_index.html#a3bd9db935c5805ab8dea473c2819058a">BamIndex::IndexType</a> Type(<span class="keywordtype">void</span>) <span class="keyword">const</span> =0;</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="comment">// internal methods</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">protected</span>:</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordtype">void</span> SetErrorString(<span class="keyword">const</span> std::string& where, <span class="keyword">const</span> std::string& what)<span class="keyword"> const </span>{</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  m_errorString = where + <span class="stringliteral">": "</span> + what;</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</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">// data members</span></div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">protected</span>:</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  Internal::BamReaderPrivate* m_reader; <span class="comment">// copy, not owned</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keyword">mutable</span> std::string m_errorString;</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> };</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="preprocessor">#endif // BAM_INDEX_H</span></div><div class="ttc" id="_bam_aux_8h_html"><div class="ttname"><a href="_bam_aux_8h.html">BamAux.h</a></div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_index_html_a8e3594d367918d5ed1187f950868f66c"><div class="ttname"><a href="class_bam_tools_1_1_bam_index.html#a8e3594d367918d5ed1187f950868f66c">BamTools::BamIndex::GetErrorString</a></div><div class="ttdeci">std::string GetErrorString(void)</div><div class="ttdef"><b>Definition:</b> BamIndex.h:55</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_index_html_a891299c6f89d3c7d1da5286e612f9a96"><div class="ttname"><a href="class_bam_tools_1_1_bam_index.html#a891299c6f89d3c7d1da5286e612f9a96">BamTools::BamIndex::~BamIndex</a></div><div class="ttdeci">virtual ~BamIndex(void)</div><div class="ttdef"><b>Definition:</b> BamIndex.h:47</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_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="class_bam_tools_1_1_bam_index_html_add9e57706ae2057b0e2ee39c5953c073"><div class="ttname"><a href="class_bam_tools_1_1_bam_index.html#add9e57706ae2057b0e2ee39c5953c073">BamTools::BamIndex::BamIndex</a></div><div class="ttdeci">BamIndex(Internal::BamReaderPrivate *reader)</div><div class="ttdef"><b>Definition:</b> BamIndex.h:46</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_index_html"><div class="ttname"><a href="class_bam_tools_1_1_bam_index.html">BamTools::BamIndex</a></div><div class="ttdoc">Provides methods for generating & loading BAM index files. </div><div class="ttdef"><b>Definition:</b> BamIndex.h:34</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="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
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