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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><li class="navelem"><a class="el" href="dir_32b1f2a912cd337a7fc75a5cc25b3a09.html">algorithms</a></li> </ul>
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<a href="_sort_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">// Sort.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">// All rights reserved.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">// Last modified: 4 April 2012 (DB)</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// Provides sorting functionality.</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> </div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#ifndef ALGORITHMS_SORT_H</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#define ALGORITHMS_SORT_H</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> </div><div class="line"><a name="l00014"></a><span class="lineno"> 14</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="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include "<a class="code" href="_bam_alignment_8h.html">api/BamAlignment.h</a>"</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include "<a class="code" href="_bam_reader_8h.html">api/BamReader.h</a>"</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include "<a class="code" href="_bam_multi_reader_8h.html">api/BamMultiReader.h</a>"</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <cassert></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <algorithm></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <functional></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html"> 24</a></span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="namespace_bam_tools_1_1_algorithms.html"> 25</a></span> <span class="keyword">namespace </span>Algorithms {</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html"> 30</a></span> <span class="keyword">struct </span><a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html">Sort</a> {</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00033"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61"> 33</a></span>  <span class="keyword">enum</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Order</a> { AscendingOrder = 0</div><div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd"> 34</a></span>  , DescendingOrder</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> </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keyword">template</span><<span class="keyword">typename</span> ElemType></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> sort_helper(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a>& order, <span class="keyword">const</span> ElemType& lhs, <span class="keyword">const</span> ElemType& rhs) {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordflow">switch</span> ( order ) {</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordflow">case</span> ( <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0">Sort::AscendingOrder</a> ) : { std::less<ElemType> comp; <span class="keywordflow">return</span> comp(lhs, rhs); }</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordflow">case</span> ( <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd">Sort::DescendingOrder</a> ) : { std::greater<ElemType> comp; <span class="keywordflow">return</span> comp(lhs, rhs); }</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  default : BT_ASSERT_UNREACHABLE;</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="keywordflow">return</span> <span class="keyword">false</span>; <span class="comment">// <-- unreachable</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  }</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keyword">typedef</span> std::binary_function<BamAlignment, BamAlignment, bool> AlignmentSortBase;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html"> 71</a></span>  <span class="keyword">struct </span><a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html">ByName</a> : <span class="keyword">public</span> AlignmentSortBase {</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="comment">// ctor</span></div><div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#a08564b85c02b48c8a95860ef2420dcda"> 74</a></span>  <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#a08564b85c02b48c8a95860ef2420dcda">ByName</a>(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a>& order = <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0">Sort::AscendingOrder</a>)</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  : m_order(order)</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  { }</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="comment">// comparison function</span></div><div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#a50c6514c7c650bb34466ff235117040b"> 79</a></span>  <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#a50c6514c7c650bb34466ff235117040b">operator()</a>(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>& lhs, <span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>& rhs) {</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordflow">return</span> sort_helper(m_order, lhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a723d7d4ff011c2e8cb612f96cbc53daf">Name</a>, rhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a723d7d4ff011c2e8cb612f96cbc53daf">Name</a>);</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  }</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="comment">// used by BamMultiReader internals</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> UsesCharData(<span class="keywordtype">void</span>) { <span class="keywordflow">return</span> <span class="keyword">true</span>; }</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a> m_order;</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> </div><div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html"> 107</a></span>  <span class="keyword">struct </span><a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html">ByPosition</a> : <span class="keyword">public</span> AlignmentSortBase {</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="comment">// ctor</span></div><div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#abad8e7fe87b39ed1d06eea4ef8fb3ac4"> 110</a></span>  <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#abad8e7fe87b39ed1d06eea4ef8fb3ac4">ByPosition</a>(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a>& order = <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0">Sort::AscendingOrder</a>)</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  : m_order(order)</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> </div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="comment">// comparison function</span></div><div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#a5e20ac05eb7a1b3ebe83725334770ff4"> 115</a></span>  <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#a5e20ac05eb7a1b3ebe83725334770ff4">operator()</a>(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>& lhs, <span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>& rhs) {</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">// force unmapped aligmnents to end</span></div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordflow">if</span> ( lhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a> == -1 ) <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordflow">if</span> ( rhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a> == -1 ) <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="comment">// if on same reference, sort on position</span></div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">if</span> ( lhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a> == rhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a> )</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordflow">return</span> sort_helper(m_order, lhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#add167f68b38bab397a10a28708ca55cc">Position</a>, rhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#add167f68b38bab397a10a28708ca55cc">Position</a>);</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">// otherwise sort on reference ID</span></div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordflow">return</span> sort_helper(m_order, lhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a>, rhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a>);</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  }</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="comment">// used by BamMultiReader internals</span></div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> UsesCharData(<span class="keywordtype">void</span>) { <span class="keywordflow">return</span> <span class="keyword">false</span>; }</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a> m_order;</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  };</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html"> 154</a></span>  <span class="keyword">struct </span><a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html">ByTag</a> : <span class="keyword">public</span> AlignmentSortBase {</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span> </div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="comment">// ctor</span></div><div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#aaca046c10c1fb4cf52dbbca81872ec94"> 157</a></span>  <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#aaca046c10c1fb4cf52dbbca81872ec94">ByTag</a>(<span class="keyword">const</span> std::string& tag,</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a>& order = <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0">Sort::AscendingOrder</a>)</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  : m_tag(tag)</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  , m_order(order)</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  { }</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> </div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="comment">// comparison function</span></div><div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#af6359624c1749b75615a098d2fc8f1c4"> 164</a></span>  <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#af6359624c1749b75615a098d2fc8f1c4">operator()</a>(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>& lhs, <span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>& rhs) {</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// force alignments without tag to end</span></div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  T lhsTagValue;</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  T rhsTagValue;</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordflow">if</span> ( !lhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f">GetTag</a>(m_tag, lhsTagValue) ) <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">if</span> ( !rhs.<a class="code" href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f">GetTag</a>(m_tag, rhsTagValue) ) <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="comment">// otherwise compare on tag values</span></div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">return</span> sort_helper(m_order, lhsTagValue, rhsTagValue);</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  }</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="comment">// used by BamMultiReader internals</span></div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> UsesCharData(<span class="keywordtype">void</span>) { <span class="keywordflow">return</span> <span class="keyword">true</span>; }</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span> </div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keyword">const</span> std::string m_tag;</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">Sort::Order</a> m_order;</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  };</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div><div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html"> 196</a></span>  <span class="keyword">struct </span><a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html">Unsorted</a> : <span class="keyword">public</span> AlignmentSortBase {</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="comment">// comparison function</span></div><div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html#ae7d272c34af22496ef4aa8233cd34b0e"> 199</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html#ae7d272c34af22496ef4aa8233cd34b0e">operator()</a>(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>&, <span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamTools::BamAlignment</a>&) {</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>; <span class="comment">// returning false tends to retain insertion order</span></div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  }</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="comment">// used by BamMultiReader internals</span></div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> UsesCharData(<span class="keywordtype">void</span>) { <span class="keywordflow">return</span> <span class="keyword">false</span>; }</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  };</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keyword">template</span><<span class="keyword">typename</span> Compare></div><div class="line"><a name="l00221"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a978c463fbbacae4a0369f8681f7b00d2"> 221</a></span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a978c463fbbacae4a0369f8681f7b00d2">SortAlignments</a>(std::vector<BamAlignment>& data,</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keyword">const</span> Compare& comp = Compare())</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  {</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  std::sort(data.begin(), data.end(), comp);</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  }</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keyword">template</span><<span class="keyword">typename</span> Compare></div><div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a9b8bd9b54fbc591462d46a502d8489d1"> 243</a></span>  <span class="keyword">static</span> <span class="keyword">inline</span> std::vector<BamAlignment> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a9b8bd9b54fbc591462d46a502d8489d1">SortAlignments</a>(<span class="keyword">const</span> std::vector<BamAlignment>& input,</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keyword">const</span> Compare& comp = Compare())</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  {</div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  std::vector<BamAlignment> output(input);</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  SortAlignments(output, comp);</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordflow">return</span> output;</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  }</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span> </div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keyword">template</span><<span class="keyword">typename</span> Compare></div><div class="line"><a name="l00272"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#aa564c7366c033d59d81d7a58d0fb6e05"> 272</a></span>  <span class="keyword">static</span> std::vector<BamAlignment> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#aa564c7366c033d59d81d7a58d0fb6e05">GetSortedRegion</a>(<a class="code" href="class_bam_tools_1_1_bam_reader.html">BamReader</a>& reader,</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <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="l00274"></a><span class="lineno"> 274</span>  <span class="keyword">const</span> Compare& comp = Compare())</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  {</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="comment">// return empty container if unable to find region</span></div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">if</span> ( !reader.<a class="code" href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5">IsOpen</a>() ) <span class="keywordflow">return</span> std::vector<BamAlignment>();</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <span class="keywordflow">if</span> ( !reader.<a class="code" href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420">SetRegion</a>(region) ) <span class="keywordflow">return</span> std::vector<BamAlignment>();</div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <span class="comment">// iterate through region, grabbing alignments</span></div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> al;</div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  std::vector<BamAlignment> results;</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordflow">while</span> ( reader.<a class="code" href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95">GetNextAlignmentCore</a>(al) )</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  results.push_back(al);</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="comment">// sort & return alignments</span></div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  SortAlignments(results, comp);</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordflow">return</span> results;</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  }</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span> </div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keyword">template</span><<span class="keyword">typename</span> Compare></div><div class="line"><a name="l00312"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#acaaab81442cd152a6460af9ffd8244d2"> 312</a></span>  <span class="keyword">static</span> std::vector<BamAlignment> <a class="code" href="struct_bam_tools_1_1_algorithms_1_1_sort.html#acaaab81442cd152a6460af9ffd8244d2">GetSortedRegion</a>(<a class="code" href="class_bam_tools_1_1_bam_multi_reader.html">BamMultiReader</a>& reader,</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <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="l00314"></a><span class="lineno"> 314</span>  <span class="keyword">const</span> Compare& comp = Compare())</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  {</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="comment">// return empty container if unable to find region</span></div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <span class="keywordflow">if</span> ( !reader.<a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#abbeb7137ba90a1851d424fffd924d7e3">HasOpenReaders</a>() ) <span class="keywordflow">return</span> std::vector<BamAlignment>();</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="keywordflow">if</span> ( !reader.<a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7">SetRegion</a>(region) ) <span class="keywordflow">return</span> std::vector<BamAlignment>();</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span> </div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="comment">// iterate through region, grabbing alignments</span></div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> al;</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  std::vector<BamAlignment> results;</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="keywordflow">while</span> ( reader.<a class="code" href="class_bam_tools_1_1_bam_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2">GetNextAlignmentCore</a>(al) )</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  results.push_back(al);</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span> </div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="comment">// sort & return alignments</span></div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  SortAlignments(results, comp);</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="keywordflow">return</span> results;</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  }</div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span> };</div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span> </div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span> } <span class="comment">// namespace Algorithms</span></div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span> <span class="preprocessor">#endif // ALGORITHMS_SORT_H</span></div><div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html_ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61aad318af311e94e010e964ee73968f8b0">BamTools::Algorithms::Sort::AscendingOrder</a></div><div class="ttdef"><b>Definition:</b> Sort.h:33</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html_acaaab81442cd152a6460af9ffd8244d2"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#acaaab81442cd152a6460af9ffd8244d2">BamTools::Algorithms::Sort::GetSortedRegion</a></div><div class="ttdeci">static std::vector< BamAlignment > GetSortedRegion(BamMultiReader &reader, const BamRegion &region, const Compare &comp=Compare())</div><div class="ttdef"><b>Definition:</b> Sort.h:312</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name_html_a50c6514c7c650bb34466ff235117040b"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#a50c6514c7c650bb34466ff235117040b">BamTools::Algorithms::Sort::ByName::operator()</a></div><div class="ttdeci">bool operator()(const BamTools::BamAlignment &lhs, const BamTools::BamAlignment &rhs)</div><div class="ttdef"><b>Definition:</b> Sort.h:79</div></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="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag_html"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html">BamTools::Algorithms::Sort::ByTag</a></div><div class="ttdoc">Function object for comparing alignments by tag value. </div><div class="ttdef"><b>Definition:</b> Sort.h:154</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag_html_aaca046c10c1fb4cf52dbbca81872ec94"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#aaca046c10c1fb4cf52dbbca81872ec94">BamTools::Algorithms::Sort::ByTag::ByTag</a></div><div class="ttdeci">ByTag(const std::string &tag, const Sort::Order &order=Sort::AscendingOrder)</div><div class="ttdef"><b>Definition:</b> Sort.h:157</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html_aa564c7366c033d59d81d7a58d0fb6e05"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#aa564c7366c033d59d81d7a58d0fb6e05">BamTools::Algorithms::Sort::GetSortedRegion</a></div><div class="ttdeci">static std::vector< BamAlignment > GetSortedRegion(BamReader &reader, const BamRegion &region, const Compare &comp=Compare())</div><div class="ttdef"><b>Definition:</b> Sort.h:272</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="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name_html"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html">BamTools::Algorithms::Sort::ByName</a></div><div class="ttdoc">Function object for comparing alignments by name. </div><div class="ttdef"><b>Definition:</b> Sort.h:71</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a257e1faa0f2dc36666e0163fff93e54f"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f">BamTools::BamAlignment::GetTag</a></div><div class="ttdeci">bool GetTag(const std::string &tag, T &destination) const</div><div class="ttdef"><b>Definition:</b> BamAlignment.h:417</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted_html_ae7d272c34af22496ef4aa8233cd34b0e"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html#ae7d272c34af22496ef4aa8233cd34b0e">BamTools::Algorithms::Sort::Unsorted::operator()</a></div><div class="ttdeci">bool operator()(const BamTools::BamAlignment &, const BamTools::BamAlignment &)</div><div class="ttdef"><b>Definition:</b> Sort.h:199</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag_html_af6359624c1749b75615a098d2fc8f1c4"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_tag.html#af6359624c1749b75615a098d2fc8f1c4">BamTools::Algorithms::Sort::ByTag::operator()</a></div><div class="ttdeci">bool operator()(const BamTools::BamAlignment &lhs, const BamTools::BamAlignment &rhs)</div><div class="ttdef"><b>Definition:</b> Sort.h:164</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_multi_reader_html_a7c9c3d1f9882053af4cbfebfb894b8c7"><div class="ttname"><a href="class_bam_tools_1_1_bam_multi_reader.html#a7c9c3d1f9882053af4cbfebfb894b8c7">BamTools::BamMultiReader::SetRegion</a></div><div class="ttdeci">bool SetRegion(const BamRegion &region)</div><div class="ttdoc">Sets a target region of interest. </div><div class="ttdef"><b>Definition:</b> BamMultiReader.cpp:391</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_reader_html"><div class="ttname"><a href="class_bam_tools_1_1_bam_reader.html">BamTools::BamReader</a></div><div class="ttdoc">Provides read access to BAM files. </div><div class="ttdef"><b>Definition:</b> BamReader.h:25</div></div>
<div class="ttc" id="_bam_alignment_8h_html"><div class="ttname"><a href="_bam_alignment_8h.html">BamAlignment.h</a></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="class_bam_tools_1_1_bam_reader_html_ac95d20470a02a104990f5a8cf9868f95"><div class="ttname"><a href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95">BamTools::BamReader::GetNextAlignmentCore</a></div><div class="ttdeci">bool GetNextAlignmentCore(BamAlignment &alignment)</div><div class="ttdoc">Retrieves next available alignment, without populating the alignment&#39;s string data fields...</div><div class="ttdef"><b>Definition:</b> BamReader.cpp:181</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html_a978c463fbbacae4a0369f8681f7b00d2"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a978c463fbbacae4a0369f8681f7b00d2">BamTools::Algorithms::Sort::SortAlignments</a></div><div class="ttdeci">static void SortAlignments(std::vector< BamAlignment > &data, const Compare &comp=Compare())</div><div class="ttdef"><b>Definition:</b> Sort.h:221</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_reader_html_ab29989c9627f2a379d4b80f9a7f349c5"><div class="ttname"><a href="class_bam_tools_1_1_bam_reader.html#ab29989c9627f2a379d4b80f9a7f349c5">BamTools::BamReader::IsOpen</a></div><div class="ttdeci">bool IsOpen(void) const</div><div class="ttdoc">Returns true if a BAM file is open for reading. </div><div class="ttdef"><b>Definition:</b> BamReader.cpp:221</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position_html"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html">BamTools::Algorithms::Sort::ByPosition</a></div><div class="ttdoc">Function object for comparing alignments by position. </div><div class="ttdef"><b>Definition:</b> Sort.h:107</div></div>
<div class="ttc" id="_bam_multi_reader_8h_html"><div class="ttname"><a href="_bam_multi_reader_8h.html">BamMultiReader.h</a></div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_add167f68b38bab397a10a28708ca55cc"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#add167f68b38bab397a10a28708ca55cc">BamTools::BamAlignment::Position</a></div><div class="ttdeci">int32_t Position</div><div class="ttdoc">position (0-based) where alignment starts </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:124</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position_html_a5e20ac05eb7a1b3ebe83725334770ff4"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#a5e20ac05eb7a1b3ebe83725334770ff4">BamTools::Algorithms::Sort::ByPosition::operator()</a></div><div class="ttdeci">bool operator()(const BamTools::BamAlignment &lhs, const BamTools::BamAlignment &rhs)</div><div class="ttdef"><b>Definition:</b> Sort.h:115</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a723d7d4ff011c2e8cb612f96cbc53daf"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a723d7d4ff011c2e8cb612f96cbc53daf">BamTools::BamAlignment::Name</a></div><div class="ttdeci">std::string Name</div><div class="ttdoc">read name </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:117</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted_html"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_unsorted.html">BamTools::Algorithms::Sort::Unsorted</a></div><div class="ttdoc">Placeholder function object. </div><div class="ttdef"><b>Definition:</b> Sort.h:196</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html">BamTools::Algorithms::Sort</a></div><div class="ttdoc">Provides classes & methods related to sorting BamAlignments. </div><div class="ttdef"><b>Definition:</b> Sort.h:30</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html_a9b8bd9b54fbc591462d46a502d8489d1"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#a9b8bd9b54fbc591462d46a502d8489d1">BamTools::Algorithms::Sort::SortAlignments</a></div><div class="ttdeci">static std::vector< BamAlignment > SortAlignments(const std::vector< BamAlignment > &input, const Compare &comp=Compare())</div><div class="ttdef"><b>Definition:</b> Sort.h:243</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_multi_reader_html_abbeb7137ba90a1851d424fffd924d7e3"><div class="ttname"><a href="class_bam_tools_1_1_bam_multi_reader.html#abbeb7137ba90a1851d424fffd924d7e3">BamTools::BamMultiReader::HasOpenReaders</a></div><div class="ttdeci">bool HasOpenReaders(void) const</div><div class="ttdoc">Returns true if there are any open BAM files. </div><div class="ttdef"><b>Definition:</b> BamMultiReader.cpp:231</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position_html_abad8e7fe87b39ed1d06eea4ef8fb3ac4"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_position.html#abad8e7fe87b39ed1d06eea4ef8fb3ac4">BamTools::Algorithms::Sort::ByPosition::ByPosition</a></div><div class="ttdeci">ByPosition(const Sort::Order &order=Sort::AscendingOrder)</div><div class="ttdef"><b>Definition:</b> Sort.h:110</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_reader_html_a1273d2e1da19861ffdc1bddeb9152420"><div class="ttname"><a href="class_bam_tools_1_1_bam_reader.html#a1273d2e1da19861ffdc1bddeb9152420">BamTools::BamReader::SetRegion</a></div><div class="ttdeci">bool SetRegion(const BamRegion &region)</div><div class="ttdoc">Sets a target region of interest. </div><div class="ttdef"><b>Definition:</b> BamReader.cpp:353</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_multi_reader_html_a7c1b307ac78087f8174b1dcac838f6a2"><div class="ttname"><a href="class_bam_tools_1_1_bam_multi_reader.html#a7c1b307ac78087f8174b1dcac838f6a2">BamTools::BamMultiReader::GetNextAlignmentCore</a></div><div class="ttdeci">bool GetNextAlignmentCore(BamAlignment &alignment)</div><div class="ttdoc">Retrieves next available alignment. </div><div class="ttdef"><b>Definition:</b> BamMultiReader.cpp:188</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="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name_html_a08564b85c02b48c8a95860ef2420dcda"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort_1_1_by_name.html#a08564b85c02b48c8a95860ef2420dcda">BamTools::Algorithms::Sort::ByName::ByName</a></div><div class="ttdeci">ByName(const Sort::Order &order=Sort::AscendingOrder)</div><div class="ttdef"><b>Definition:</b> Sort.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="struct_bam_tools_1_1_algorithms_1_1_sort_html_ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61a551ab4e6dbb5a38344515ca0823b8ddd">BamTools::Algorithms::Sort::DescendingOrder</a></div><div class="ttdef"><b>Definition:</b> Sort.h:34</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a5e4b74de5a5d6cd3f74a5466505b97b6"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">BamTools::BamAlignment::RefID</a></div><div class="ttdeci">int32_t RefID</div><div class="ttdoc">ID number for reference sequence. </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:123</div></div>
<div class="ttc" id="struct_bam_tools_1_1_algorithms_1_1_sort_html_ab00bd07c176b33933717ca362b716f61"><div class="ttname"><a href="struct_bam_tools_1_1_algorithms_1_1_sort.html#ab00bd07c176b33933717ca362b716f61">BamTools::Algorithms::Sort::Order</a></div><div class="ttdeci">Order</div><div class="ttdoc">Provides explicit values for specifying desired sort ordering. </div><div class="ttdef"><b>Definition:</b> Sort.h:33</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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