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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_aux_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">// BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg</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: 25 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 data structures & utility methods that are used throughout the API.</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 BAMAUX_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define BAMAUX_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 <cstring></span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include <fstream></span> </div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <iostream></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 <vector></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> </div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// ----------------------------------------------------------------</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="comment">// CigarOp</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div><div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_cigar_op.html"> 41</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_cigar_op.html">CigarOp</a> {</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  </div><div class="line"><a name="l00043"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_cigar_op.html#afd1ea1fa2eb044569c301157137dcb82"> 43</a></span>  <span class="keywordtype">char</span> <a class="code" href="struct_bam_tools_1_1_cigar_op.html#afd1ea1fa2eb044569c301157137dcb82">Type</a>; </div><div class="line"><a name="l00044"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_cigar_op.html#ae71433a878279710557a154b29b4bb17"> 44</a></span>  uint32_t <a class="code" href="struct_bam_tools_1_1_cigar_op.html#ae71433a878279710557a154b29b4bb17">Length</a>; </div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  </div><div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_cigar_op.html#a7ad38f6f438ca690e80e919ffa8a28ef"> 47</a></span>  <a class="code" href="struct_bam_tools_1_1_cigar_op.html#a7ad38f6f438ca690e80e919ffa8a28ef">CigarOp</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> type = <span class="charliteral">'\0'</span>, </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">const</span> uint32_t& length = 0)</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  : Type(type)</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  , Length(length) </div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  { }</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> };</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">// ----------------------------------------------------------------</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment">// RefData</span></div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_ref_data.html"> 60</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_ref_data.html">RefData</a> {</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  </div><div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_ref_data.html#a06dc4dd6f05bed1531234d49180a8402"> 62</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_ref_data.html#a06dc4dd6f05bed1531234d49180a8402">RefName</a>; </div><div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_ref_data.html#aaca9e72fa1855228910b9e6e274f3b45"> 63</a></span>  int32_t <a class="code" href="struct_bam_tools_1_1_ref_data.html#aaca9e72fa1855228910b9e6e274f3b45">RefLength</a>; </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  </div><div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_ref_data.html#af89dff8a9f7e7d80bb53b29cef9a7e6a"> 66</a></span>  <a class="code" href="struct_bam_tools_1_1_ref_data.html#af89dff8a9f7e7d80bb53b29cef9a7e6a">RefData</a>(<span class="keyword">const</span> std::string& name = <span class="stringliteral">""</span>,</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">const</span> int32_t& length = 0)</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  : RefName(name)</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  , RefLength(length)</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  { }</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> };</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div><div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573"> 74</a></span> <span class="keyword">typedef</span> std::vector<RefData> <a class="code" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a>;</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">// BamRegion</span></div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html"> 88</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_bam_region.html">BamRegion</a> {</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  </div><div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a34bfcf995c20986e3a7442974cba137c"> 90</a></span>  <span class="keywordtype">int</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a34bfcf995c20986e3a7442974cba137c">LeftRefID</a>; </div><div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a8c84513d817b590b74b64399acc178e5"> 91</a></span>  <span class="keywordtype">int</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a8c84513d817b590b74b64399acc178e5">LeftPosition</a>; </div><div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a1e11c35bce33870dc0c65019bfe886b1"> 92</a></span>  <span class="keywordtype">int</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a1e11c35bce33870dc0c65019bfe886b1">RightRefID</a>; </div><div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a71ce3b72e5e6f74022e21055a3dd3d93"> 93</a></span>  <span class="keywordtype">int</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a71ce3b72e5e6f74022e21055a3dd3d93">RightPosition</a>; </div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  </div><div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a5b7922dee81342a9b073e9ad3561ce37"> 96</a></span>  <a class="code" href="struct_bam_tools_1_1_bam_region.html#a5b7922dee81342a9b073e9ad3561ce37">BamRegion</a>(<span class="keyword">const</span> <span class="keywordtype">int</span>& leftID = -1, </div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>& leftPos = -1,</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>& rightID = -1,</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>& rightPos = -1)</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  : LeftRefID(leftID)</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  , LeftPosition(leftPos)</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  , RightRefID(rightID)</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  , RightPosition(rightPos)</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  { }</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  </div><div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a73685728dcf8eadb5192e34932b2a1ee"> 107</a></span>  <a class="code" href="struct_bam_tools_1_1_bam_region.html#a73685728dcf8eadb5192e34932b2a1ee">BamRegion</a>(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html">BamRegion</a>& other)</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  : LeftRefID(other.LeftRefID)</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  , LeftPosition(other.LeftPosition)</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  , RightRefID(other.RightRefID)</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  , RightPosition(other.RightPosition)</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="l00115"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a7f94a21e6b0602dedd9aa30b76e44f72"> 115</a></span>  <span class="keywordtype">void</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a7f94a21e6b0602dedd9aa30b76e44f72">clear</a>(<span class="keywordtype">void</span>) {</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  LeftRefID = -1; LeftPosition = -1;</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  RightRefID = -1; RightPosition = -1;</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  }</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a47922a2ea611d809a5e84dea65cd8ab8"> 121</a></span>  <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a47922a2ea611d809a5e84dea65cd8ab8">isLeftBoundSpecified</a>(<span class="keywordtype">void</span>)<span class="keyword"> const </span>{</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">return</span> ( LeftRefID >= 0 && LeftPosition >= 0 );</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="l00126"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a379117ba981ba25cb5bd2fbaf9da3aa0"> 126</a></span>  <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a379117ba981ba25cb5bd2fbaf9da3aa0">isNull</a>(<span class="keywordtype">void</span>)<span class="keyword"> const </span>{</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">return</span> ( !isLeftBoundSpecified() && !isRightBoundSpecified() );</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> </div><div class="line"><a name="l00131"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_bam_region.html#a478526892e3c9e18f09ce707702b32a8"> 131</a></span>  <span class="keywordtype">bool</span> <a class="code" href="struct_bam_tools_1_1_bam_region.html#a478526892e3c9e18f09ce707702b32a8">isRightBoundSpecified</a>(<span class="keywordtype">void</span>)<span class="keyword"> const </span>{</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">return</span> ( RightRefID >= 0 && RightPosition >= 1 );</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  }</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> };</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div><div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_custom_header_tag.html"> 136</a></span> <span class="keyword">struct </span><a class="code" href="struct_bam_tools_1_1_custom_header_tag.html">CustomHeaderTag</a> {</div><div class="line"><a name="l00137"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_custom_header_tag.html#a1b07d0c2224366774af35bd893d84050"> 137</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_custom_header_tag.html#a1b07d0c2224366774af35bd893d84050">TagName</a>;</div><div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_custom_header_tag.html#a0c03f1fd9b59174bac1f18df5f98e337"> 138</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_custom_header_tag.html#a0c03f1fd9b59174bac1f18df5f98e337">TagValue</a>;</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> };</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="comment">// ----------------------------------------------------------------</span></div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment">// General utility methods</span></div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div><div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a5c866cd2fe41ae6ae22be9d544abcdeb"> 148</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="namespace_bam_tools.html#a5c866cd2fe41ae6ae22be9d544abcdeb">FileExists</a>(<span class="keyword">const</span> std::string& filename) {</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  std::ifstream f(filename.c_str(), std::ifstream::in);</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordflow">return</span> !f.fail();</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> }</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div><div class="line"><a name="l00156"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#af8c7d17bddec46961e82dc5bfd009c55"> 156</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#af8c7d17bddec46961e82dc5bfd009c55">SwapEndian_16</a>(int16_t& x) {</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  x = ((x >> 8) | (x << 8));</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span> }</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div><div class="line"><a name="l00163"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#abebe62e0746f698db30b1681ef27b64a"> 163</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#af8c7d17bddec46961e82dc5bfd009c55">SwapEndian_16</a>(uint16_t& x) {</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  x = ((x >> 8) | (x << 8));</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> </div><div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a79bfc085656a840d548e81443cbe110a"> 170</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a79bfc085656a840d548e81443cbe110a">SwapEndian_32</a>(int32_t& x) {</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  x = ( (x >> 24) | </div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  ((x << 8) & 0x00FF0000) | </div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  ((x >> 8) & 0x0000FF00) | </div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  (x << 24)</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> }</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span> </div><div class="line"><a name="l00181"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a320480630cac81dd4818bbb379468b94"> 181</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a79bfc085656a840d548e81443cbe110a">SwapEndian_32</a>(uint32_t& x) {</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  x = ( (x >> 24) | </div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  ((x << 8) & 0x00FF0000) | </div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  ((x >> 8) & 0x0000FF00) | </div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  (x << 24)</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  );</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span> }</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span> </div><div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a9ff814335b08775504f458b77d65e2ce"> 192</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a9ff814335b08775504f458b77d65e2ce">SwapEndian_64</a>(int64_t& x) {</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  x = ( (x >> 56) | </div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  ((x << 40) & 0x00FF000000000000ll) |</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  ((x << 24) & 0x0000FF0000000000ll) |</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  ((x << 8) & 0x000000FF00000000ll) |</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  ((x >> 8) & 0x00000000FF000000ll) |</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  ((x >> 24) & 0x0000000000FF0000ll) |</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  ((x >> 40) & 0x000000000000FF00ll) |</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  (x << 56)</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> </div><div class="line"><a name="l00207"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#aca95615fe69f82f5b0a8c8e3ef81f76c"> 207</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a9ff814335b08775504f458b77d65e2ce">SwapEndian_64</a>(uint64_t& x) {</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  x = ( (x >> 56) | </div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  ((x << 40) & 0x00FF000000000000ll) |</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  ((x << 24) & 0x0000FF0000000000ll) |</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  ((x << 8) & 0x000000FF00000000ll) |</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  ((x >> 8) & 0x00000000FF000000ll) |</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  ((x >> 24) & 0x0000000000FF0000ll) |</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  ((x >> 40) & 0x000000000000FF00ll) |</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  (x << 56)</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  );</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span> }</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div><div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a30ca8d29f22f7a1298279a44fa058a89"> 222</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a30ca8d29f22f7a1298279a44fa058a89">SwapEndian_16p</a>(<span class="keywordtype">char</span>* data) {</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  uint16_t& value = (uint16_t&)*data; </div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <a class="code" href="namespace_bam_tools.html#af8c7d17bddec46961e82dc5bfd009c55">SwapEndian_16</a>(value);</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="l00230"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a050d8622d5683412459129f5cdfc0510"> 230</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a050d8622d5683412459129f5cdfc0510">SwapEndian_32p</a>(<span class="keywordtype">char</span>* data) {</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  uint32_t& value = (uint32_t&)*data; </div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <a class="code" href="namespace_bam_tools.html#a79bfc085656a840d548e81443cbe110a">SwapEndian_32</a>(value);</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span> }</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div><div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a98cbc5937c70207a63fa2efdb35f06ab"> 238</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a98cbc5937c70207a63fa2efdb35f06ab">SwapEndian_64p</a>(<span class="keywordtype">char</span>* data) {</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  uint64_t& value = (uint64_t&)*data; </div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <a class="code" href="namespace_bam_tools.html#a9ff814335b08775504f458b77d65e2ce">SwapEndian_64</a>(value);</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span> }</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div><div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ae094562e5e79ba0ee051e39ef770dce6"> 247</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="namespace_bam_tools.html#ae094562e5e79ba0ee051e39ef770dce6">SystemIsBigEndian</a>(<span class="keywordtype">void</span>) {</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keyword">const</span> uint16_t one = 0x0001;</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordflow">return</span> ((*(<span class="keywordtype">char</span>*) &one) == 0 );</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span> }</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div><div class="line"><a name="l00258"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a53750928dd60a51f81fd89c050f1fc27"> 258</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#a53750928dd60a51f81fd89c050f1fc27">PackUnsignedInt</a>(<span class="keywordtype">char</span>* buffer, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> value) {</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  buffer[0] = (char)value;</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  buffer[1] = (char)(value >> 8);</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  buffer[2] = (char)(value >> 16);</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  buffer[3] = (char)(value >> 24);</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span> }</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div><div class="line"><a name="l00271"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ae312a004460f1d311050aee20948fe30"> 271</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="namespace_bam_tools.html#ae312a004460f1d311050aee20948fe30">PackUnsignedShort</a>(<span class="keywordtype">char</span>* buffer, <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> value) {</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  buffer[0] = (char)value;</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  buffer[1] = (char)(value >> 8);</div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span> }</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span> </div><div class="line"><a name="l00282"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ae8ff80b95685561a3f64390e99a13eb6"> 282</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="namespace_bam_tools.html#ae8ff80b95685561a3f64390e99a13eb6">UnpackDouble</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keyword">union </span>{ <span class="keywordtype">double</span> value; <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(double)]; } un;</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  un.value = 0;</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  un.valueBuffer[0] = buffer[0];</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  un.valueBuffer[1] = buffer[1];</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  un.valueBuffer[2] = buffer[2];</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  un.valueBuffer[3] = buffer[3];</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  un.valueBuffer[4] = buffer[4];</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  un.valueBuffer[5] = buffer[5];</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  un.valueBuffer[6] = buffer[6];</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  un.valueBuffer[7] = buffer[7];</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordflow">return</span> un.value;</div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span> }</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span> </div><div class="line"><a name="l00304"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#afe7a4c87b171950a215ff9e100e5bc25"> 304</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="namespace_bam_tools.html#ae8ff80b95685561a3f64390e99a13eb6">UnpackDouble</a>(<span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="keywordflow">return</span> <a class="code" href="namespace_bam_tools.html#ae8ff80b95685561a3f64390e99a13eb6">UnpackDouble</a>( (<span class="keyword">const</span> <span class="keywordtype">char</span>*)buffer );</div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span> }</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span> </div><div class="line"><a name="l00314"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ab48c404191e8d4b994234ac28f61fd62"> 314</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">float</span> <a class="code" href="namespace_bam_tools.html#ab48c404191e8d4b994234ac28f61fd62">UnpackFloat</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="keyword">union </span>{ <span class="keywordtype">float</span> value; <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(float)]; } un;</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  un.value = 0;</div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  un.valueBuffer[0] = buffer[0];</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  un.valueBuffer[1] = buffer[1];</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  un.valueBuffer[2] = buffer[2];</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  un.valueBuffer[3] = buffer[3];</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keywordflow">return</span> un.value;</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span> }</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div><div class="line"><a name="l00332"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a83ec76e074db1d1e577d9ac402ef38f5"> 332</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">float</span> <a class="code" href="namespace_bam_tools.html#ab48c404191e8d4b994234ac28f61fd62">UnpackFloat</a>(<span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="keywordflow">return</span> <a class="code" href="namespace_bam_tools.html#ab48c404191e8d4b994234ac28f61fd62">UnpackFloat</a>( (<span class="keyword">const</span> <span class="keywordtype">char</span>*)buffer );</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> </div><div class="line"><a name="l00342"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a22411da6d7641153e91878d0d406cf2e"> 342</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">signed</span> <span class="keywordtype">int</span> <a class="code" href="namespace_bam_tools.html#a22411da6d7641153e91878d0d406cf2e">UnpackSignedInt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keyword">union </span>{ <span class="keywordtype">signed</span> <span class="keywordtype">int</span> value; <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(<span class="keywordtype">signed</span> int)]; } un;</div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  un.value = 0;</div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  un.valueBuffer[0] = buffer[0];</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  un.valueBuffer[1] = buffer[1];</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  un.valueBuffer[2] = buffer[2];</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  un.valueBuffer[3] = buffer[3];</div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">return</span> un.value;</div><div class="line"><a name="l00350"></a><span class="lineno"> 350</span> }</div><div class="line"><a name="l00351"></a><span class="lineno"> 351</span> </div><div class="line"><a name="l00360"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ac5769b06ba414888fd219ab04790db8e"> 360</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">signed</span> <span class="keywordtype">int</span> <a class="code" href="namespace_bam_tools.html#a22411da6d7641153e91878d0d406cf2e">UnpackSignedInt</a>(<span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="keywordflow">return</span> <a class="code" href="namespace_bam_tools.html#a22411da6d7641153e91878d0d406cf2e">UnpackSignedInt</a>( (<span class="keyword">const</span> <span class="keywordtype">char</span>*) buffer );</div><div class="line"><a name="l00362"></a><span class="lineno"> 362</span> }</div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span> </div><div class="line"><a name="l00370"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a45b0b642522cd5daa01b5975b1c0b0fb"> 370</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">signed</span> <span class="keywordtype">short</span> <a class="code" href="namespace_bam_tools.html#a45b0b642522cd5daa01b5975b1c0b0fb">UnpackSignedShort</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keyword">union </span>{ <span class="keywordtype">signed</span> <span class="keywordtype">short</span> value; <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(<span class="keywordtype">signed</span> short)]; } un;</div><div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  un.value = 0;</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span> <span class="preprocessor">#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__</span></div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  un.valueBuffer[0] = buffer[0];</div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  un.valueBuffer[1] = buffer[1];</div><div class="line"><a name="l00376"></a><span class="lineno"> 376</span> <span class="preprocessor">#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__</span></div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  un.valueBuffer[0] = buffer[1];</div><div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  un.valueBuffer[1] = buffer[0];</div><div class="line"><a name="l00379"></a><span class="lineno"> 379</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00380"></a><span class="lineno"> 380</span> <span class="preprocessor"> #error "Unsupported hardware"</span></div><div class="line"><a name="l00381"></a><span class="lineno"> 381</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <span class="keywordflow">return</span> un.value;</div><div class="line"><a name="l00383"></a><span class="lineno"> 383</span> }</div><div class="line"><a name="l00384"></a><span class="lineno"> 384</span> </div><div class="line"><a name="l00393"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ab1cf624abaf114a6987507531475e500"> 393</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">signed</span> <span class="keywordtype">short</span> <a class="code" href="namespace_bam_tools.html#a45b0b642522cd5daa01b5975b1c0b0fb">UnpackSignedShort</a>(<span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="keywordflow">return</span> <a class="code" href="namespace_bam_tools.html#a45b0b642522cd5daa01b5975b1c0b0fb">UnpackSignedShort</a>( (<span class="keyword">const</span> <span class="keywordtype">char</span>*)buffer );</div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span> }</div><div class="line"><a name="l00396"></a><span class="lineno"> 396</span> </div><div class="line"><a name="l00403"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a301bcd05554045ea18fe358225566ff2"> 403</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="namespace_bam_tools.html#a301bcd05554045ea18fe358225566ff2">UnpackUnsignedInt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <span class="keyword">union </span>{ <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> value; <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(<span class="keywordtype">unsigned</span> int)]; } un;</div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  un.value = 0;</div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  un.valueBuffer[0] = buffer[0];</div><div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  un.valueBuffer[1] = buffer[1];</div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  un.valueBuffer[2] = buffer[2];</div><div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  un.valueBuffer[3] = buffer[3];</div><div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordflow">return</span> un.value;</div><div class="line"><a name="l00411"></a><span class="lineno"> 411</span> }</div><div class="line"><a name="l00412"></a><span class="lineno"> 412</span> </div><div class="line"><a name="l00421"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ad5f9933ed32ad75fd0f434dbfbc61638"> 421</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="namespace_bam_tools.html#a301bcd05554045ea18fe358225566ff2">UnpackUnsignedInt</a>(<span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordflow">return</span> <a class="code" href="namespace_bam_tools.html#a301bcd05554045ea18fe358225566ff2">UnpackUnsignedInt</a>( (<span class="keyword">const</span> <span class="keywordtype">char</span>*)buffer );</div><div class="line"><a name="l00423"></a><span class="lineno"> 423</span> }</div><div class="line"><a name="l00424"></a><span class="lineno"> 424</span> </div><div class="line"><a name="l00431"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#aa8dccd65248544654a8cee1dc521c2d2"> 431</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <a class="code" href="namespace_bam_tools.html#aa8dccd65248544654a8cee1dc521c2d2">UnpackUnsignedShort</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keyword">union </span>{ <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> value; <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(<span class="keywordtype">unsigned</span> short)]; } un;</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  un.value = 0;</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span> <span class="preprocessor">#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__</span></div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  un.valueBuffer[0] = buffer[0];</div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  un.valueBuffer[1] = buffer[1];</div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span> <span class="preprocessor">#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__</span></div><div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  un.valueBuffer[0] = buffer[1];</div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  un.valueBuffer[1] = buffer[0];</div><div class="line"><a name="l00440"></a><span class="lineno"> 440</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00441"></a><span class="lineno"> 441</span> <span class="preprocessor"> #error "Unsupported hardware"</span></div><div class="line"><a name="l00442"></a><span class="lineno"> 442</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keywordflow">return</span> un.value;</div><div class="line"><a name="l00444"></a><span class="lineno"> 444</span> }</div><div class="line"><a name="l00445"></a><span class="lineno"> 445</span> </div><div class="line"><a name="l00454"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a4d44d4ccf1c4d76d678ef670e205c684"> 454</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <a class="code" href="namespace_bam_tools.html#aa8dccd65248544654a8cee1dc521c2d2">UnpackUnsignedShort</a>(<span class="keywordtype">char</span>* buffer) {</div><div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  <span class="keywordflow">return</span> <a class="code" href="namespace_bam_tools.html#aa8dccd65248544654a8cee1dc521c2d2">UnpackUnsignedShort</a>( (<span class="keyword">const</span> <span class="keywordtype">char</span>*)buffer );</div><div class="line"><a name="l00456"></a><span class="lineno"> 456</span> }</div><div class="line"><a name="l00457"></a><span class="lineno"> 457</span> </div><div class="line"><a name="l00458"></a><span class="lineno"> 458</span> <span class="comment">// ----------------------------------------------------------------</span></div><div class="line"><a name="l00459"></a><span class="lineno"> 459</span> <span class="comment">// 'internal' helper structs</span></div><div class="line"><a name="l00460"></a><span class="lineno"> 460</span> </div><div class="line"><a name="l00464"></a><span class="lineno"> 464</span> <span class="keyword">struct </span>RaiiBuffer {</div><div class="line"><a name="l00465"></a><span class="lineno"> 465</span> </div><div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="keywordtype">char</span>* Buffer;</div><div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <span class="keyword">const</span> <span class="keywordtype">size_t</span> NumBytes;</div><div class="line"><a name="l00469"></a><span class="lineno"> 469</span> </div><div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="comment">// ctor & dtor</span></div><div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  RaiiBuffer(<span class="keyword">const</span> <span class="keywordtype">size_t</span> n)</div><div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  : Buffer( <span class="keyword">new</span> <span class="keywordtype">char</span>[n]() )</div><div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  , NumBytes(n)</div><div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  { }</div><div class="line"><a name="l00475"></a><span class="lineno"> 475</span> </div><div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  ~RaiiBuffer(<span class="keywordtype">void</span>) {</div><div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="keyword">delete</span>[] Buffer;</div><div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  }</div><div class="line"><a name="l00479"></a><span class="lineno"> 479</span> </div><div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="comment">// add'l methods</span></div><div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="keywordtype">void</span> Clear(<span class="keywordtype">void</span>) {</div><div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  memset(Buffer, 0, NumBytes);</div><div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  }</div><div class="line"><a name="l00484"></a><span class="lineno"> 484</span> };</div><div class="line"><a name="l00485"></a><span class="lineno"> 485</span> </div><div class="line"><a name="l00486"></a><span class="lineno"> 486</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00487"></a><span class="lineno"> 487</span> </div><div class="line"><a name="l00488"></a><span class="lineno"> 488</span> <span class="preprocessor">#endif // BAMAUX_H</span></div><div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a1e11c35bce33870dc0c65019bfe886b1"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a1e11c35bce33870dc0c65019bfe886b1">BamTools::BamRegion::RightRefID</a></div><div class="ttdeci">int RightRefID</div><div class="ttdoc">reference ID for region&#39;s right boundary </div><div class="ttdef"><b>Definition:</b> BamAux.h:92</div></div>
<div class="ttc" id="namespace_bam_tools_html_a45b0b642522cd5daa01b5975b1c0b0fb"><div class="ttname"><a href="namespace_bam_tools.html#a45b0b642522cd5daa01b5975b1c0b0fb">BamTools::UnpackSignedShort</a></div><div class="ttdeci">API_EXPORT signed short UnpackSignedShort(const char *buffer)</div><div class="ttdoc">reads a signed short integer value from byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:370</div></div>
<div class="ttc" id="namespace_bam_tools_html_ae8ff80b95685561a3f64390e99a13eb6"><div class="ttname"><a href="namespace_bam_tools.html#ae8ff80b95685561a3f64390e99a13eb6">BamTools::UnpackDouble</a></div><div class="ttdeci">API_EXPORT double UnpackDouble(const char *buffer)</div><div class="ttdoc">reads a double value from byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:282</div></div>
<div class="ttc" id="namespace_bam_tools_html_a050d8622d5683412459129f5cdfc0510"><div class="ttname"><a href="namespace_bam_tools.html#a050d8622d5683412459129f5cdfc0510">BamTools::SwapEndian_32p</a></div><div class="ttdeci">API_EXPORT void SwapEndian_32p(char *data)</div><div class="ttdoc">swaps endianness of the next 4 bytes in a buffer, in place </div><div class="ttdef"><b>Definition:</b> BamAux.h:230</div></div>
<div class="ttc" id="namespace_bam_tools_html_a301bcd05554045ea18fe358225566ff2"><div class="ttname"><a href="namespace_bam_tools.html#a301bcd05554045ea18fe358225566ff2">BamTools::UnpackUnsignedInt</a></div><div class="ttdeci">API_EXPORT unsigned int UnpackUnsignedInt(const char *buffer)</div><div class="ttdoc">reads an unsigned integer value from byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:403</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_bam_region_html_a379117ba981ba25cb5bd2fbaf9da3aa0"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a379117ba981ba25cb5bd2fbaf9da3aa0">BamTools::BamRegion::isNull</a></div><div class="ttdeci">bool isNull(void) const</div><div class="ttdoc">Returns true if region boundaries are not defined. </div><div class="ttdef"><b>Definition:</b> BamAux.h:126</div></div>
<div class="ttc" id="namespace_bam_tools_html_ab48c404191e8d4b994234ac28f61fd62"><div class="ttname"><a href="namespace_bam_tools.html#ab48c404191e8d4b994234ac28f61fd62">BamTools::UnpackFloat</a></div><div class="ttdeci">API_EXPORT float UnpackFloat(const char *buffer)</div><div class="ttdoc">reads a float value from byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:314</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a8c84513d817b590b74b64399acc178e5"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a8c84513d817b590b74b64399acc178e5">BamTools::BamRegion::LeftPosition</a></div><div class="ttdeci">int LeftPosition</div><div class="ttdoc">position for region&#39;s left boundary </div><div class="ttdef"><b>Definition:</b> BamAux.h:91</div></div>
<div class="ttc" id="namespace_bam_tools_html_a5c866cd2fe41ae6ae22be9d544abcdeb"><div class="ttname"><a href="namespace_bam_tools.html#a5c866cd2fe41ae6ae22be9d544abcdeb">BamTools::FileExists</a></div><div class="ttdeci">API_EXPORT bool FileExists(const std::string &filename)</div><div class="ttdoc">returns true if the file exists </div><div class="ttdef"><b>Definition:</b> BamAux.h:148</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a47922a2ea611d809a5e84dea65cd8ab8"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a47922a2ea611d809a5e84dea65cd8ab8">BamTools::BamRegion::isLeftBoundSpecified</a></div><div class="ttdeci">bool isLeftBoundSpecified(void) const</div><div class="ttdoc">Returns true if region has a left boundary. </div><div class="ttdef"><b>Definition:</b> BamAux.h:121</div></div>
<div class="ttc" id="struct_bam_tools_1_1_cigar_op_html_a7ad38f6f438ca690e80e919ffa8a28ef"><div class="ttname"><a href="struct_bam_tools_1_1_cigar_op.html#a7ad38f6f438ca690e80e919ffa8a28ef">BamTools::CigarOp::CigarOp</a></div><div class="ttdeci">CigarOp(const char type='\0', const uint32_t &length=0)</div><div class="ttdoc">constructor </div><div class="ttdef"><b>Definition:</b> BamAux.h:47</div></div>
<div class="ttc" id="namespace_bam_tools_html_a79bfc085656a840d548e81443cbe110a"><div class="ttname"><a href="namespace_bam_tools.html#a79bfc085656a840d548e81443cbe110a">BamTools::SwapEndian_32</a></div><div class="ttdeci">API_EXPORT void SwapEndian_32(int32_t &x)</div><div class="ttdoc">swaps endianness of signed 32-bit integer, in place </div><div class="ttdef"><b>Definition:</b> BamAux.h:170</div></div>
<div class="ttc" id="namespace_bam_tools_html_a22411da6d7641153e91878d0d406cf2e"><div class="ttname"><a href="namespace_bam_tools.html#a22411da6d7641153e91878d0d406cf2e">BamTools::UnpackSignedInt</a></div><div class="ttdeci">API_EXPORT signed int UnpackSignedInt(const char *buffer)</div><div class="ttdoc">reads a signed integer value from byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:342</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="namespace_bam_tools_html_ae312a004460f1d311050aee20948fe30"><div class="ttname"><a href="namespace_bam_tools.html#ae312a004460f1d311050aee20948fe30">BamTools::PackUnsignedShort</a></div><div class="ttdeci">API_EXPORT void PackUnsignedShort(char *buffer, unsigned short value)</div><div class="ttdoc">stores unsigned short integer value in a byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:271</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a34bfcf995c20986e3a7442974cba137c"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a34bfcf995c20986e3a7442974cba137c">BamTools::BamRegion::LeftRefID</a></div><div class="ttdeci">int LeftRefID</div><div class="ttdoc">reference ID for region&#39;s left boundary </div><div class="ttdef"><b>Definition:</b> BamAux.h:90</div></div>
<div class="ttc" id="namespace_bam_tools_html_a30ca8d29f22f7a1298279a44fa058a89"><div class="ttname"><a href="namespace_bam_tools.html#a30ca8d29f22f7a1298279a44fa058a89">BamTools::SwapEndian_16p</a></div><div class="ttdeci">API_EXPORT void SwapEndian_16p(char *data)</div><div class="ttdoc">swaps endianness of the next 2 bytes in a buffer, in place </div><div class="ttdef"><b>Definition:</b> BamAux.h:222</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a5b7922dee81342a9b073e9ad3561ce37"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a5b7922dee81342a9b073e9ad3561ce37">BamTools::BamRegion::BamRegion</a></div><div class="ttdeci">BamRegion(const int &leftID=-1, const int &leftPos=-1, const int &rightID=-1, const int &rightPos=-1)</div><div class="ttdoc">constructor </div><div class="ttdef"><b>Definition:</b> BamAux.h:96</div></div>
<div class="ttc" id="struct_bam_tools_1_1_cigar_op_html_afd1ea1fa2eb044569c301157137dcb82"><div class="ttname"><a href="struct_bam_tools_1_1_cigar_op.html#afd1ea1fa2eb044569c301157137dcb82">BamTools::CigarOp::Type</a></div><div class="ttdeci">char Type</div><div class="ttdoc">CIGAR operation type (MIDNSHPX=) </div><div class="ttdef"><b>Definition:</b> BamAux.h:43</div></div>
<div class="ttc" id="struct_bam_tools_1_1_ref_data_html_a06dc4dd6f05bed1531234d49180a8402"><div class="ttname"><a href="struct_bam_tools_1_1_ref_data.html#a06dc4dd6f05bed1531234d49180a8402">BamTools::RefData::RefName</a></div><div class="ttdeci">std::string RefName</div><div class="ttdoc">name of reference sequence </div><div class="ttdef"><b>Definition:</b> BamAux.h:62</div></div>
<div class="ttc" id="struct_bam_tools_1_1_cigar_op_html"><div class="ttname"><a href="struct_bam_tools_1_1_cigar_op.html">BamTools::CigarOp</a></div><div class="ttdoc">Represents a CIGAR alignment operation. </div><div class="ttdef"><b>Definition:</b> BamAux.h:41</div></div>
<div class="ttc" id="struct_bam_tools_1_1_custom_header_tag_html_a0c03f1fd9b59174bac1f18df5f98e337"><div class="ttname"><a href="struct_bam_tools_1_1_custom_header_tag.html#a0c03f1fd9b59174bac1f18df5f98e337">BamTools::CustomHeaderTag::TagValue</a></div><div class="ttdeci">std::string TagValue</div><div class="ttdef"><b>Definition:</b> BamAux.h:138</div></div>
<div class="ttc" id="namespace_bam_tools_html_a9ff814335b08775504f458b77d65e2ce"><div class="ttname"><a href="namespace_bam_tools.html#a9ff814335b08775504f458b77d65e2ce">BamTools::SwapEndian_64</a></div><div class="ttdeci">API_EXPORT void SwapEndian_64(int64_t &x)</div><div class="ttdoc">swaps endianness of signed 64-bit integer, in place </div><div class="ttdef"><b>Definition:</b> BamAux.h:192</div></div>
<div class="ttc" id="struct_bam_tools_1_1_ref_data_html_af89dff8a9f7e7d80bb53b29cef9a7e6a"><div class="ttname"><a href="struct_bam_tools_1_1_ref_data.html#af89dff8a9f7e7d80bb53b29cef9a7e6a">BamTools::RefData::RefData</a></div><div class="ttdeci">RefData(const std::string &name="", const int32_t &length=0)</div><div class="ttdoc">constructor </div><div class="ttdef"><b>Definition:</b> BamAux.h:66</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a73685728dcf8eadb5192e34932b2a1ee"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a73685728dcf8eadb5192e34932b2a1ee">BamTools::BamRegion::BamRegion</a></div><div class="ttdeci">BamRegion(const BamRegion &other)</div><div class="ttdoc">copy constructor </div><div class="ttdef"><b>Definition:</b> BamAux.h:107</div></div>
<div class="ttc" id="namespace_bam_tools_html_a98cbc5937c70207a63fa2efdb35f06ab"><div class="ttname"><a href="namespace_bam_tools.html#a98cbc5937c70207a63fa2efdb35f06ab">BamTools::SwapEndian_64p</a></div><div class="ttdeci">API_EXPORT void SwapEndian_64p(char *data)</div><div class="ttdoc">swaps endianness of the next 8 bytes in a buffer, in place </div><div class="ttdef"><b>Definition:</b> BamAux.h:238</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a71ce3b72e5e6f74022e21055a3dd3d93"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a71ce3b72e5e6f74022e21055a3dd3d93">BamTools::BamRegion::RightPosition</a></div><div class="ttdeci">int RightPosition</div><div class="ttdoc">position for region&#39;s right boundary </div><div class="ttdef"><b>Definition:</b> BamAux.h:93</div></div>
<div class="ttc" id="struct_bam_tools_1_1_ref_data_html"><div class="ttname"><a href="struct_bam_tools_1_1_ref_data.html">BamTools::RefData</a></div><div class="ttdoc">Represents a reference sequence entry. </div><div class="ttdef"><b>Definition:</b> BamAux.h:60</div></div>
<div class="ttc" id="struct_bam_tools_1_1_ref_data_html_aaca9e72fa1855228910b9e6e274f3b45"><div class="ttname"><a href="struct_bam_tools_1_1_ref_data.html#aaca9e72fa1855228910b9e6e274f3b45">BamTools::RefData::RefLength</a></div><div class="ttdeci">int32_t RefLength</div><div class="ttdoc">length of reference sequence </div><div class="ttdef"><b>Definition:</b> BamAux.h:63</div></div>
<div class="ttc" id="struct_bam_tools_1_1_cigar_op_html_ae71433a878279710557a154b29b4bb17"><div class="ttname"><a href="struct_bam_tools_1_1_cigar_op.html#ae71433a878279710557a154b29b4bb17">BamTools::CigarOp::Length</a></div><div class="ttdeci">uint32_t Length</div><div class="ttdoc">CIGAR operation length (number of bases) </div><div class="ttdef"><b>Definition:</b> BamAux.h:44</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a7f94a21e6b0602dedd9aa30b76e44f72"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a7f94a21e6b0602dedd9aa30b76e44f72">BamTools::BamRegion::clear</a></div><div class="ttdeci">void clear(void)</div><div class="ttdoc">Clears region boundaries. </div><div class="ttdef"><b>Definition:</b> BamAux.h:115</div></div>
<div class="ttc" id="namespace_bam_tools_html_a53750928dd60a51f81fd89c050f1fc27"><div class="ttname"><a href="namespace_bam_tools.html#a53750928dd60a51f81fd89c050f1fc27">BamTools::PackUnsignedInt</a></div><div class="ttdeci">API_EXPORT void PackUnsignedInt(char *buffer, unsigned int value)</div><div class="ttdoc">stores unsigned integer value in a byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:258</div></div>
<div class="ttc" id="namespace_bam_tools_html_ae094562e5e79ba0ee051e39ef770dce6"><div class="ttname"><a href="namespace_bam_tools.html#ae094562e5e79ba0ee051e39ef770dce6">BamTools::SystemIsBigEndian</a></div><div class="ttdeci">API_EXPORT bool SystemIsBigEndian(void)</div><div class="ttdoc">checks host architecture&#39;s byte order </div><div class="ttdef"><b>Definition:</b> BamAux.h:247</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_af8c7d17bddec46961e82dc5bfd009c55"><div class="ttname"><a href="namespace_bam_tools.html#af8c7d17bddec46961e82dc5bfd009c55">BamTools::SwapEndian_16</a></div><div class="ttdeci">API_EXPORT void SwapEndian_16(int16_t &x)</div><div class="ttdoc">swaps endianness of signed 16-bit integer, in place </div><div class="ttdef"><b>Definition:</b> BamAux.h:156</div></div>
<div class="ttc" id="struct_bam_tools_1_1_bam_region_html_a478526892e3c9e18f09ce707702b32a8"><div class="ttname"><a href="struct_bam_tools_1_1_bam_region.html#a478526892e3c9e18f09ce707702b32a8">BamTools::BamRegion::isRightBoundSpecified</a></div><div class="ttdeci">bool isRightBoundSpecified(void) const</div><div class="ttdoc">Returns true if region has a right boundary. </div><div class="ttdef"><b>Definition:</b> BamAux.h:131</div></div>
<div class="ttc" id="struct_bam_tools_1_1_custom_header_tag_html_a1b07d0c2224366774af35bd893d84050"><div class="ttname"><a href="struct_bam_tools_1_1_custom_header_tag.html#a1b07d0c2224366774af35bd893d84050">BamTools::CustomHeaderTag::TagName</a></div><div class="ttdeci">std::string TagName</div><div class="ttdef"><b>Definition:</b> BamAux.h:137</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="namespace_bam_tools_html_aa8dccd65248544654a8cee1dc521c2d2"><div class="ttname"><a href="namespace_bam_tools.html#aa8dccd65248544654a8cee1dc521c2d2">BamTools::UnpackUnsignedShort</a></div><div class="ttdeci">API_EXPORT unsigned short UnpackUnsignedShort(const char *buffer)</div><div class="ttdoc">reads an unsigned short integer value from byte buffer </div><div class="ttdef"><b>Definition:</b> BamAux.h:431</div></div>
<div class="ttc" id="struct_bam_tools_1_1_custom_header_tag_html"><div class="ttname"><a href="struct_bam_tools_1_1_custom_header_tag.html">BamTools::CustomHeaderTag</a></div><div class="ttdef"><b>Definition:</b> BamAux.h:136</div></div>
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