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<a href="_bam_alignment_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">// BamAlignment.h (c) 2009 Derek Barnett</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// Marth Lab, Department of Biology, Boston College</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// Last modified: 25 July 2013 (DB)</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// Provides the BamAlignment data structure</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 BAMALIGNMENT_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define BAMALIGNMENT_H</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "<a class="code" href="api__global_8h.html">api/api_global.h</a>"</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "<a class="code" href="_bam_aux_8h.html">api/BamAux.h</a>"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include "<a class="code" href="_bam_constants_8h.html">api/BamConstants.h</a>"</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include <cstdlib></span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include <cstring></span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// forward declaration of BamAlignment's "friends"</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">namespace </span>Internal {</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="keyword">class </span>BamReaderPrivate;</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keyword">class </span>BamWriterPrivate;</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> } <span class="comment">// namespace Internal</span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment"></span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// BamAlignment data structure</span></div><div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html"> 32</a></span> <span class="keyword">class </span><a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> {</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="comment">// constructors & destructor</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>& other);</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  ~<a class="code" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="comment">// queries against alignment flags</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">public</span>: </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordtype">bool</span> IsDuplicate(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if this read is a PCR duplicate</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordtype">bool</span> IsFailedQC(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if this read failed quality control</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">bool</span> IsFirstMate(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment is first mate on read</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">bool</span> IsMapped(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment is mapped</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordtype">bool</span> IsMateMapped(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment's mate is mapped</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordtype">bool</span> IsMateReverseStrand(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment's mate mapped to reverse strand</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">bool</span> IsPaired(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment part of paired-end read</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">bool</span> IsPrimaryAlignment(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if reported position is primary alignment</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordtype">bool</span> IsProperPair(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment is part of read that satisfied paired-end resolution</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordtype">bool</span> IsReverseStrand(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment mapped to reverse strand</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordtype">bool</span> IsSecondMate(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment is second mate on read</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">// manipulate alignment flags</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keyword">public</span>: </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">void</span> SetIsDuplicate(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "PCR duplicate" flag</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordtype">void</span> SetIsFailedQC(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "failed quality control" flag</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordtype">void</span> SetIsFirstMate(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment is first mate" flag</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">void</span> SetIsMapped(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment is mapped" flag</span></div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordtype">void</span> SetIsMateMapped(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment's mate is mapped" flag</span></div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordtype">void</span> SetIsMateReverseStrand(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment's mate mapped to reverse strand" flag</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordtype">void</span> SetIsPaired(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment part of paired-end read" flag</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordtype">void</span> SetIsPrimaryAlignment(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "position is primary alignment" flag</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordtype">void</span> SetIsProperPair(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment is part of read that satisfied paired-end resolution" flag</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordtype">void</span> SetIsReverseStrand(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment mapped to reverse strand" flag</span></div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordtype">void</span> SetIsSecondMate(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of "alignment is second mate on read" flag</span></div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="comment">// tag data access methods</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keyword">public</span>:</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>  <span class="comment">// add a new tag</span></div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">bool</span> AddTag(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::string& type, <span class="keyword">const</span> T& value);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">bool</span> AddTag(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::vector<T>& values);</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="comment">// edit (or append) tag</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">bool</span> EditTag(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::string& type, <span class="keyword">const</span> T& value);</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">bool</span> EditTag(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::vector<T>& values);</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="comment">// retrieves tag data</span></div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">bool</span> GetTag(<span class="keyword">const</span> std::string& tag, T& destination) <span class="keyword">const</span>;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">bool</span> GetTag(<span class="keyword">const</span> std::string& tag, std::vector<T>& destination) <span class="keyword">const</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">// retrieves all current tag names</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  std::vector<std::string> GetTagNames(<span class="keywordtype">void</span>) <span class="keyword">const</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">// retrieves the SAM/BAM type-code for requested tag name</span></div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">bool</span> GetTagType(<span class="keyword">const</span> std::string& tag, <span class="keywordtype">char</span>& type) <span class="keyword">const</span>;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="comment">// retrieves the SAM/BAM type-code for the data elements in an array tag</span></div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">bool</span> GetArrayTagType(<span class="keyword">const</span> std::string& tag, <span class="keywordtype">char</span>& type) <span class="keyword">const</span>;</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="comment">// returns true if alignment has a record for this tag name</span></div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordtype">bool</span> HasTag(<span class="keyword">const</span> std::string& tag) <span class="keyword">const</span>;</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="comment">// removes a tag</span></div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordtype">void</span> RemoveTag(<span class="keyword">const</span> std::string& tag);</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="comment">// additional methods</span></div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">// populates alignment string fields</span></div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">bool</span> BuildCharData(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// calculates alignment end position</span></div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">int</span> GetEndPosition(<span class="keywordtype">bool</span> usePadded = <span class="keyword">false</span>, <span class="keywordtype">bool</span> closedInterval = <span class="keyword">false</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">// returns a description of the last error that occurred</span></div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  std::string GetErrorString(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</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">// retrieves the size, read locations and reference locations of soft-clip operations</span></div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">bool</span> GetSoftClips(std::vector<int>& clipSizes,</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  std::vector<int>& readPositions,</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  std::vector<int>& genomePositions,</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">bool</span> usePadded = <span class="keyword">false</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="comment">// public data fields</span></div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a723d7d4ff011c2e8cb612f96cbc53daf"> 117</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a723d7d4ff011c2e8cb612f96cbc53daf">Name</a>; <span class="comment">// read name</span></div><div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a4d2ee5aeba57fdffc36e8fb9e01c4bb4"> 118</a></span>  int32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a4d2ee5aeba57fdffc36e8fb9e01c4bb4">Length</a>; <span class="comment">// length of query sequence</span></div><div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#aed5682a27b7bc660d45d705e4411b3d5"> 119</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#aed5682a27b7bc660d45d705e4411b3d5">QueryBases</a>; <span class="comment">// 'original' sequence (contained in BAM file)</span></div><div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a55d27086aca3e321cee411d43633a788"> 120</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a55d27086aca3e321cee411d43633a788">AlignedBases</a>; <span class="comment">// 'aligned' sequence (QueryBases plus deletion, padding, clipping chars)</span></div><div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a9af49d39bda11b60eb12ed4162100fd6"> 121</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a9af49d39bda11b60eb12ed4162100fd6">Qualities</a>; <span class="comment">// FASTQ qualities (ASCII characters, not numeric values)</span></div><div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#ab3ac5fc4c4f193d0448882e592a31962"> 122</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#ab3ac5fc4c4f193d0448882e592a31962">TagData</a>; <span class="comment">// tag data (use provided methods to query/modify)</span></div><div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6"> 123</a></span>  int32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a5e4b74de5a5d6cd3f74a5466505b97b6">RefID</a>; <span class="comment">// ID number for reference sequence</span></div><div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#add167f68b38bab397a10a28708ca55cc"> 124</a></span>  int32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#add167f68b38bab397a10a28708ca55cc">Position</a>; <span class="comment">// position (0-based) where alignment starts</span></div><div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#aa7068d3ba7704dbecb6b47ffbf6f8467"> 125</a></span>  uint16_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#aa7068d3ba7704dbecb6b47ffbf6f8467">Bin</a>; <span class="comment">// BAM (standard) index bin number for this alignment</span></div><div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a96c235eb7645c6e0fcf5da5bfb16a2aa"> 126</a></span>  uint16_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a96c235eb7645c6e0fcf5da5bfb16a2aa">MapQuality</a>; <span class="comment">// mapping quality score</span></div><div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a528e10f19aec995e58ec7dbdf1e35b6b"> 127</a></span>  uint32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a528e10f19aec995e58ec7dbdf1e35b6b">AlignmentFlag</a>; <span class="comment">// alignment bit-flag (use provided methods to query/modify)</span></div><div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#ac7ad2244a0e268abdcdf09e97fadee3e"> 128</a></span>  std::vector<CigarOp> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#ac7ad2244a0e268abdcdf09e97fadee3e">CigarData</a>; <span class="comment">// CIGAR operations for this alignment</span></div><div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#acbfdd5b968249c9c074943b2d1fddca8"> 129</a></span>  int32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#acbfdd5b968249c9c074943b2d1fddca8">MateRefID</a>; <span class="comment">// ID number for reference sequence where alignment's mate was aligned</span></div><div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#aaef8a38689198150d0627a51b53e6352"> 130</a></span>  int32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#aaef8a38689198150d0627a51b53e6352">MatePosition</a>; <span class="comment">// position (0-based) where alignment's mate starts</span></div><div class="line"><a name="l00131"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a19c45c67919fb8d22d3487b3f1fcd79d"> 131</a></span>  int32_t <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a19c45c67919fb8d22d3487b3f1fcd79d">InsertSize</a>; <span class="comment">// mate-pair insert size</span></div><div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#abbac2cbd8b0508c36a6be13ab1aa53c4"> 132</a></span>  std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#abbac2cbd8b0508c36a6be13ab1aa53c4">Filename</a>; <span class="comment">// name of BAM file which this alignment comes from</span></div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// internal utility methods</span></div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordtype">bool</span> FindTag(<span class="keyword">const</span> std::string& tag,</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordtype">char</span>*& pTagData,</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>& tagDataLength,</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>& numBytesParsed) <span class="keyword">const</span>;</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordtype">bool</span> IsValidSize(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::string& type) <span class="keyword">const</span>;</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordtype">void</span> SetErrorString(<span class="keyword">const</span> std::string& where, <span class="keyword">const</span> std::string& what) <span class="keyword">const</span>;</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordtype">bool</span> SkipToNextTag(<span class="keyword">const</span> <span class="keywordtype">char</span> storageType,</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordtype">char</span>*& pTagData,</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>& numBytesParsed) <span class="keyword">const</span>;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="comment">// internal data</span></div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keyword">struct </span>BamAlignmentSupportData {</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  std::string AllCharData;</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  uint32_t BlockLength;</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  uint32_t NumCigarOperations;</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  uint32_t QueryNameLength;</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  uint32_t QuerySequenceLength;</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordtype">bool</span> HasCoreOnly;</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">// constructor</span></div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  BamAlignmentSupportData(<span class="keywordtype">void</span>)</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  : BlockLength(0)</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  , NumCigarOperations(0)</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  , QueryNameLength(0)</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  , QuerySequenceLength(0)</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  , HasCoreOnly(false)</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  { }</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  };</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  BamAlignmentSupportData SupportData;</div><div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a1ff3357da3472115c30e9b3285502bbf"> 172</a></span>  <span class="keyword">friend</span> <span class="keyword">class </span>Internal::BamReaderPrivate;</div><div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#aa01fcc0bfc0452beb435289c61d8dec8"> 173</a></span>  <span class="keyword">friend</span> <span class="keyword">class </span>Internal::BamWriterPrivate;</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>  <span class="keyword">mutable</span> std::string ErrorString; <span class="comment">// mutable to allow updates even in logically const methods</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="l00178"></a><span class="lineno"> 178</span> <span class="comment">// ---------------------------------------------------------</span></div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span> <span class="comment">// BamAlignment tag access methods</span></div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> </div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a553f81130bf6e136ae8859bb89011c71"> 193</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a553f81130bf6e136ae8859bb89011c71">BamAlignment::AddTag</a>(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::string& type, <span class="keyword">const</span> T& value) {</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="comment">// if char data not populated, do that first</span></div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  BuildCharData();</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="comment">// check tag/type size</span></div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keywordflow">if</span> ( !IsValidSize(tag, type) ) {</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  }</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="comment">// check that storage type code is OK for T</span></div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">if</span> ( !TagTypeHelper<T>::CanConvertTo(type.at(0)) ) {</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  }</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> </div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <span class="keywordtype">char</span>* pTagData = (<span class="keywordtype">char</span>*)TagData.data();</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> tagDataLength = TagData.size();</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytesParsed = 0;</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="comment">// if tag already exists, return false</span></div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="comment">// use EditTag explicitly instead</span></div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordflow">if</span> ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  }</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span> </div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="comment">// otherwise, convert value to string</span></div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keyword">union </span>{ T value; <span class="keywordtype">char</span> valueBuffer[<span class="keyword">sizeof</span>(T)]; } un;</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  un.value = value;</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="comment">// copy original tag data to temp buffer</span></div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keyword">const</span> std::string newTag = tag + type;</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="keyword">const</span> <span class="keywordtype">size_t</span> newTagDataLength = tagDataLength + newTag.size() + <span class="keyword">sizeof</span>(T); <span class="comment">// leave room for new T</span></div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  RaiiBuffer originalTagData(newTagDataLength);</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength + 1); <span class="comment">// '+1' for TagData null-term</span></div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="comment">// append newTag</span></div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  strcat(originalTagData.Buffer + tagDataLength, newTag.data());</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  memcpy(originalTagData.Buffer + tagDataLength + newTag.size(), un.valueBuffer, <span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="comment">// store temp buffer back in TagData</span></div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keyword">const</span> <span class="keywordtype">char</span>* newTagData = (<span class="keyword">const</span> <span class="keywordtype">char</span>*)originalTagData.Buffer;</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  TagData.assign(newTagData, newTagDataLength);</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</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="l00243"></a><span class="lineno"> 243</span> <span class="keyword">template</span><></div><div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ac9a7f11b4033e3f29183dce30e29b7da"> 244</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> BamAlignment::AddTag<std::string>(<span class="keyword">const</span> std::string& tag,</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keyword">const</span> std::string& type,</div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keyword">const</span> std::string& value)</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span> {</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="comment">// if char data not populated, do that first</span></div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  BuildCharData();</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="comment">// check tag/type size</span></div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">if</span> ( !IsValidSize(tag, type) ) {</div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  }</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="comment">// check that storage type code is OK for string</span></div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">if</span> ( !TagTypeHelper<std::string>::CanConvertTo(type.at(0)) ) {</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  }</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>  <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordtype">char</span>* pTagData = (<span class="keywordtype">char</span>*)TagData.data();</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> tagDataLength = TagData.size();</div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytesParsed = 0;</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span> </div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="comment">// if tag already exists, return false</span></div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="comment">// use EditTag explicitly instead</span></div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keywordflow">if</span> ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</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="l00276"></a><span class="lineno"> 276</span>  <span class="comment">// otherwise, copy tag data to temp buffer</span></div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keyword">const</span> std::string newTag = tag + type + value;</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <span class="keyword">const</span> <span class="keywordtype">size_t</span> newTagDataLength = tagDataLength + newTag.size() + 1; <span class="comment">// leave room for null-term</span></div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  RaiiBuffer originalTagData(newTagDataLength);</div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength + 1); <span class="comment">// '+1' for TagData null-term</span></div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span> </div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="comment">// append newTag (removes original null-term, then appends newTag + null-term)</span></div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  strcat(originalTagData.Buffer + tagDataLength, newTag.data());</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="comment">// store temp buffer back in TagData</span></div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="keyword">const</span> <span class="keywordtype">char</span>* newTagData = (<span class="keyword">const</span> <span class="keywordtype">char</span>*)originalTagData.Buffer;</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  TagData.assign(newTagData, newTagDataLength);</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</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="l00301"></a><span class="lineno"> 301</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00302"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#ab09155dbfea4f7ab1c86eb31ffdcae47"> 302</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a553f81130bf6e136ae8859bb89011c71">BamAlignment::AddTag</a>(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::vector<T>& values) {</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span> </div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="comment">// if char data not populated, do that first</span></div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  BuildCharData();</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span> </div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="comment">// check for valid tag name length</span></div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <span class="keywordflow">if</span> ( tag.size() != <a class="code" href="namespace_bam_tools_1_1_constants.html#a4d1b3e2b26a9d163336a4a83c62b86b7">Constants::BAM_TAG_TAGSIZE</a> )</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keywordtype">char</span>* pTagData = (<span class="keywordtype">char</span>*)TagData.data();</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> tagDataLength = TagData.size();</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytesParsed = 0;</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <span class="comment">// if tag already exists, return false</span></div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="comment">// use EditTag explicitly instead</span></div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="keywordflow">if</span> ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</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="l00324"></a><span class="lineno"> 324</span>  <span class="comment">// build new tag's base information</span></div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="keywordtype">char</span> newTagBase[<a class="code" href="namespace_bam_tools_1_1_constants.html#aff396fa749e1439449433191eae166c7">Constants::BAM_TAG_ARRAYBASE_SIZE</a>];</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  memcpy( newTagBase, tag.c_str(), <a class="code" href="namespace_bam_tools_1_1_constants.html#a4d1b3e2b26a9d163336a4a83c62b86b7">Constants::BAM_TAG_TAGSIZE</a> );</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  newTagBase[2] = <a class="code" href="namespace_bam_tools_1_1_constants.html#a53c2f04fc2e633f61e8f39264b6ad0b0">Constants::BAM_TAG_TYPE_ARRAY</a>;</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  newTagBase[3] = TagTypeHelper<T>::TypeCode();</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>  <span class="comment">// add number of array elements to newTagBase</span></div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keyword">const</span> int32_t numElements = values.size();</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  memcpy(newTagBase + 4, &numElements, <span class="keyword">sizeof</span>(int32_t));</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="comment">// copy current TagData string to temp buffer, leaving room for new tag's contents</span></div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="keyword">const</span> <span class="keywordtype">size_t</span> newTagDataLength = tagDataLength +</div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <a class="code" href="namespace_bam_tools_1_1_constants.html#aff396fa749e1439449433191eae166c7">Constants::BAM_TAG_ARRAYBASE_SIZE</a> +</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  numElements*<span class="keyword">sizeof</span>(T);</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  RaiiBuffer originalTagData(newTagDataLength);</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength+1); <span class="comment">// '+1' for TagData's null-term</span></div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span> </div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="comment">// write newTagBase (removes old null term)</span></div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  strcat(originalTagData.Buffer + tagDataLength, (<span class="keyword">const</span> <span class="keywordtype">char</span>*)newTagBase);</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="comment">// add vector elements to tag</span></div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordtype">int</span> elementsBeginOffset = tagDataLength + <a class="code" href="namespace_bam_tools_1_1_constants.html#aff396fa749e1439449433191eae166c7">Constants::BAM_TAG_ARRAYBASE_SIZE</a>;</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">for</span> ( <span class="keywordtype">int</span> i = 0 ; i < numElements; ++i ) {</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keyword">const</span> T& value = values.at(i);</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  memcpy(originalTagData.Buffer + elementsBeginOffset + i*<span class="keyword">sizeof</span>(T), &value, <span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  }</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>  <span class="comment">// store temp buffer back in TagData</span></div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="keyword">const</span> <span class="keywordtype">char</span>* newTagData = (<span class="keyword">const</span> <span class="keywordtype">char</span>*)originalTagData.Buffer;</div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  TagData.assign(newTagData, newTagDataLength);</div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00355"></a><span class="lineno"> 355</span> }</div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span> </div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00372"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#af70ac92ef127712790dff1cddfb3bccd"> 372</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#af70ac92ef127712790dff1cddfb3bccd">BamAlignment::EditTag</a>(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::string& type, <span class="keyword">const</span> T& value) {</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span> </div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  <span class="comment">// if char data not populated, do that first</span></div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  BuildCharData();</div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span> </div><div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="comment">// remove existing tag if present, then append tag with new value</span></div><div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="keywordflow">if</span> ( HasTag(tag) )</div><div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  RemoveTag(tag);</div><div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordflow">return</span> AddTag(tag, type, value);</div><div class="line"><a name="l00382"></a><span class="lineno"> 382</span> }</div><div class="line"><a name="l00383"></a><span class="lineno"> 383</span> </div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00396"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#afa96020f82b5cd0d4f0e7684026fc820"> 396</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#af70ac92ef127712790dff1cddfb3bccd">BamAlignment::EditTag</a>(<span class="keyword">const</span> std::string& tag, <span class="keyword">const</span> std::vector<T>& values) {</div><div class="line"><a name="l00397"></a><span class="lineno"> 397</span> </div><div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="comment">// if char data not populated, do that first</span></div><div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  BuildCharData();</div><div class="line"><a name="l00401"></a><span class="lineno"> 401</span> </div><div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <span class="comment">// remove existing tag if present, then append tag with new values</span></div><div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  <span class="keywordflow">if</span> ( HasTag(tag) )</div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  RemoveTag(tag);</div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="keywordflow">return</span> AddTag(tag, values);</div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span> }</div><div class="line"><a name="l00407"></a><span class="lineno"> 407</span> </div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span> </div><div class="line"><a name="l00416"></a><span class="lineno"> 416</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00417"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f"> 417</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f">BamAlignment::GetTag</a>(<span class="keyword">const</span> std::string& tag, T& destination)<span class="keyword"> const </span>{</div><div class="line"><a name="l00418"></a><span class="lineno"> 418</span> </div><div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  <span class="comment">// skip if alignment is core-only</span></div><div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly ) {</div><div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</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="l00425"></a><span class="lineno"> 425</span>  <span class="comment">// skip if no tags present</span></div><div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordflow">if</span> ( TagData.empty() ) {</div><div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  }</div><div class="line"><a name="l00430"></a><span class="lineno"> 430</span> </div><div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordtype">char</span>* pTagData = (<span class="keywordtype">char</span>*)TagData.data();</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> tagDataLength = TagData.size();</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytesParsed = 0;</div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span> </div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  <span class="comment">// return failure if tag not found</span></div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  <span class="keywordflow">if</span> ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  }</div><div class="line"><a name="l00441"></a><span class="lineno"> 441</span> </div><div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <span class="comment">// fetch data type</span></div><div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> type = *(pTagData - 1);</div><div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="keywordflow">if</span> ( !TagTypeHelper<T>::CanConvertFrom(type) ) {</div><div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="comment">// TODO: set error string ?</span></div><div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  }</div><div class="line"><a name="l00448"></a><span class="lineno"> 448</span> </div><div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="comment">// determine data length</span></div><div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  <span class="keywordtype">int</span> destinationLength = 0;</div><div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keywordflow">switch</span> ( type ) {</div><div class="line"><a name="l00452"></a><span class="lineno"> 452</span> </div><div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="comment">// 1 byte data</span></div><div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a25602acbbce34e865d67d75b9966a4fc">Constants::BAM_TAG_TYPE_ASCII</a>) :</div><div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a8cb4f3703011f90521564830a7f7df01">Constants::BAM_TAG_TYPE_INT8</a>) :</div><div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a0c4f77ed450936979e858e0703324dab">Constants::BAM_TAG_TYPE_UINT8</a>) :</div><div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  destinationLength = 1;</div><div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div><div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="comment">// 2 byte data</span></div><div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#aa51e6bf07e0ec1f00072477492d31a57">Constants::BAM_TAG_TYPE_INT16</a>) :</div><div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a9b7df792a6c644788360152e2cf56a3c">Constants::BAM_TAG_TYPE_UINT16</a>) :</div><div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  destinationLength = 2;</div><div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">break</span>;</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">// 4 byte data</span></div><div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a20a298552510340fdc2b76c496186884">Constants::BAM_TAG_TYPE_INT32</a>) :</div><div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a657c724f6561af0520aa6c2f4c23f740">Constants::BAM_TAG_TYPE_UINT32</a>) :</div><div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a5f4b4689a7898fde204f9f3275a6bcdf">Constants::BAM_TAG_TYPE_FLOAT</a>) :</div><div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  destinationLength = 4;</div><div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00472"></a><span class="lineno"> 472</span> </div><div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="comment">// var-length types not supported for numeric destination</span></div><div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a7f2d8fb36a83c9f0b14ec88100f69d62">Constants::BAM_TAG_TYPE_STRING</a>) :</div><div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a1f432cf41f5c315f8da46f302ab9cdc4">Constants::BAM_TAG_TYPE_HEX</a>) :</div><div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a53c2f04fc2e633f61e8f39264b6ad0b0">Constants::BAM_TAG_TYPE_ARRAY</a>) :</div><div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  SetErrorString(<span class="stringliteral">"BamAlignment::GetTag"</span>,</div><div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  <span class="stringliteral">"cannot store variable length tag data into a numeric destination"</span>);</div><div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00480"></a><span class="lineno"> 480</span> </div><div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="comment">// unrecognized tag type</span></div><div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  <span class="keywordflow">default</span>:</div><div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="keyword">const</span> std::string message = std::string(<span class="stringliteral">"invalid tag type: "</span>) + type;</div><div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  SetErrorString(<span class="stringliteral">"BamAlignment::GetTag"</span>, message);</div><div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00486"></a><span class="lineno"> 486</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="comment">// store data in destination</span></div><div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  destination = 0;</div><div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  memcpy(&destination, pTagData, destinationLength);</div><div class="line"><a name="l00491"></a><span class="lineno"> 491</span> </div><div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  <span class="comment">// return success</span></div><div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00494"></a><span class="lineno"> 494</span> }</div><div class="line"><a name="l00495"></a><span class="lineno"> 495</span> </div><div class="line"><a name="l00496"></a><span class="lineno"> 496</span> <span class="keyword">template</span><></div><div class="line"><a name="l00497"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a8b6c0f9db6f33bd8213304ce47a7e857"> 497</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> BamAlignment::GetTag<std::string>(<span class="keyword">const</span> std::string& tag,</div><div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  std::string& destination) <span class="keyword">const</span></div><div class="line"><a name="l00499"></a><span class="lineno"> 499</span> {</div><div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="comment">// skip if alignment is core-only</span></div><div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly ) {</div><div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  }</div><div class="line"><a name="l00505"></a><span class="lineno"> 505</span> </div><div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <span class="comment">// skip if no tags present</span></div><div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  <span class="keywordflow">if</span> ( TagData.empty() ) {</div><div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  }</div><div class="line"><a name="l00511"></a><span class="lineno"> 511</span> </div><div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  <span class="keywordtype">char</span>* pTagData = (<span class="keywordtype">char</span>*)TagData.data();</div><div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> tagDataLength = TagData.size();</div><div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytesParsed = 0;</div><div class="line"><a name="l00516"></a><span class="lineno"> 516</span> </div><div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  <span class="comment">// return failure if tag not found</span></div><div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  <span class="keywordflow">if</span> ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  }</div><div class="line"><a name="l00522"></a><span class="lineno"> 522</span> </div><div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  <span class="comment">// otherwise copy data into destination</span></div><div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> dataLength = strlen(pTagData);</div><div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  destination.clear();</div><div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  destination.resize(dataLength);</div><div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  memcpy( (<span class="keywordtype">char</span>*)destination.data(), pTagData, dataLength );</div><div class="line"><a name="l00528"></a><span class="lineno"> 528</span> </div><div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="comment">// return success</span></div><div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00531"></a><span class="lineno"> 531</span> }</div><div class="line"><a name="l00532"></a><span class="lineno"> 532</span> </div><div class="line"><a name="l00540"></a><span class="lineno"> 540</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div><div class="line"><a name="l00541"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_bam_alignment.html#a261b3a6e3f41e5d481c4d1d29e9c9371"> 541</a></span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a257e1faa0f2dc36666e0163fff93e54f">BamAlignment::GetTag</a>(<span class="keyword">const</span> std::string& tag, std::vector<T>& destination)<span class="keyword"> const </span>{</div><div class="line"><a name="l00542"></a><span class="lineno"> 542</span> </div><div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  <span class="comment">// skip if alignment is core-only</span></div><div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  <span class="keywordflow">if</span> ( SupportData.HasCoreOnly ) {</div><div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  }</div><div class="line"><a name="l00548"></a><span class="lineno"> 548</span> </div><div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  <span class="comment">// skip if no tags present</span></div><div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  <span class="keywordflow">if</span> ( TagData.empty() ) {</div><div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  }</div><div class="line"><a name="l00554"></a><span class="lineno"> 554</span> </div><div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="keywordtype">char</span>* pTagData = (<span class="keywordtype">char</span>*)TagData.data();</div><div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> tagDataLength = TagData.size();</div><div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytesParsed = 0;</div><div class="line"><a name="l00559"></a><span class="lineno"> 559</span> </div><div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  <span class="comment">// return false if tag not found</span></div><div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  <span class="keywordflow">if</span> ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  }</div><div class="line"><a name="l00565"></a><span class="lineno"> 565</span> </div><div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  <span class="comment">// check that tag is array type</span></div><div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> tagType = *(pTagData - 1);</div><div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  <span class="keywordflow">if</span> ( tagType != <a class="code" href="namespace_bam_tools_1_1_constants.html#a53c2f04fc2e633f61e8f39264b6ad0b0">Constants::BAM_TAG_TYPE_ARRAY</a> ) {</div><div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  SetErrorString(<span class="stringliteral">"BamAlignment::GetTag"</span>, <span class="stringliteral">"cannot store a non-array tag in array destination"</span>);</div><div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  }</div><div class="line"><a name="l00572"></a><span class="lineno"> 572</span> </div><div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  <span class="comment">// fetch element type</span></div><div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> elementType = *pTagData;</div><div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  <span class="keywordflow">if</span> ( !TagTypeHelper<T>::CanConvertFrom(elementType) ) {</div><div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="comment">// TODO: set error string ?</span></div><div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  }</div><div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  ++pTagData;</div><div class="line"><a name="l00580"></a><span class="lineno"> 580</span> </div><div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  <span class="comment">// calculate length of each element in tag's array</span></div><div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  <span class="keywordtype">int</span> elementLength = 0;</div><div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  <span class="keywordflow">switch</span> ( elementType ) {</div><div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a25602acbbce34e865d67d75b9966a4fc">Constants::BAM_TAG_TYPE_ASCII</a>) :</div><div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a8cb4f3703011f90521564830a7f7df01">Constants::BAM_TAG_TYPE_INT8</a>) :</div><div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a0c4f77ed450936979e858e0703324dab">Constants::BAM_TAG_TYPE_UINT8</a>) :</div><div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  elementLength = <span class="keyword">sizeof</span>(uint8_t);</div><div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00589"></a><span class="lineno"> 589</span> </div><div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#aa51e6bf07e0ec1f00072477492d31a57">Constants::BAM_TAG_TYPE_INT16</a>) :</div><div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a9b7df792a6c644788360152e2cf56a3c">Constants::BAM_TAG_TYPE_UINT16</a>) :</div><div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  elementLength = <span class="keyword">sizeof</span>(uint16_t);</div><div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00594"></a><span class="lineno"> 594</span> </div><div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a20a298552510340fdc2b76c496186884">Constants::BAM_TAG_TYPE_INT32</a>) :</div><div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a657c724f6561af0520aa6c2f4c23f740">Constants::BAM_TAG_TYPE_UINT32</a>) :</div><div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a5f4b4689a7898fde204f9f3275a6bcdf">Constants::BAM_TAG_TYPE_FLOAT</a>) :</div><div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  elementLength = <span class="keyword">sizeof</span>(uint32_t);</div><div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00600"></a><span class="lineno"> 600</span> </div><div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  <span class="comment">// var-length types not supported for numeric destination</span></div><div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a7f2d8fb36a83c9f0b14ec88100f69d62">Constants::BAM_TAG_TYPE_STRING</a>) :</div><div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a1f432cf41f5c315f8da46f302ab9cdc4">Constants::BAM_TAG_TYPE_HEX</a>) :</div><div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  <span class="keywordflow">case</span> (<a class="code" href="namespace_bam_tools_1_1_constants.html#a53c2f04fc2e633f61e8f39264b6ad0b0">Constants::BAM_TAG_TYPE_ARRAY</a>) :</div><div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  SetErrorString(<span class="stringliteral">"BamAlignment::GetTag"</span>,</div><div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  <span class="stringliteral">"invalid array data, variable-length elements are not allowed"</span>);</div><div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00608"></a><span class="lineno"> 608</span> </div><div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <span class="comment">// unknown tag type</span></div><div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <span class="keywordflow">default</span>:</div><div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  <span class="keyword">const</span> std::string message = std::string(<span class="stringliteral">"invalid array element type: "</span>) + elementType;</div><div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  SetErrorString(<span class="stringliteral">"BamAlignment::GetTag"</span>, message);</div><div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  }</div><div class="line"><a name="l00615"></a><span class="lineno"> 615</span> </div><div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  <span class="comment">// get number of elements</span></div><div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  int32_t numElements;</div><div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  memcpy(&numElements, pTagData, <span class="keyword">sizeof</span>(int32_t));</div><div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  pTagData += 4;</div><div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  destination.clear();</div><div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  destination.reserve(numElements);</div><div class="line"><a name="l00622"></a><span class="lineno"> 622</span> </div><div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  <span class="comment">// read in elements</span></div><div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  T value;</div><div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordflow">for</span> ( <span class="keywordtype">int</span> i = 0 ; i < numElements; ++i ) {</div><div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  memcpy(&value, pTagData, <span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  pTagData += <span class="keyword">sizeof</span>(T);</div><div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  destination.push_back(value);</div><div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  }</div><div class="line"><a name="l00630"></a><span class="lineno"> 630</span> </div><div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  <span class="comment">// return success</span></div><div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00633"></a><span class="lineno"> 633</span> }</div><div class="line"><a name="l00634"></a><span class="lineno"> 634</span> </div><div class="line"><a name="l00635"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a5ec8c1bc89a0c5979696a4a124fcbaeb"> 635</a></span> <span class="keyword">typedef</span> std::vector<BamAlignment> <a class="code" href="namespace_bam_tools.html#a5ec8c1bc89a0c5979696a4a124fcbaeb">BamAlignmentVector</a>;</div><div class="line"><a name="l00636"></a><span class="lineno"> 636</span> </div><div class="line"><a name="l00637"></a><span class="lineno"> 637</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00638"></a><span class="lineno"> 638</span> </div><div class="line"><a name="l00639"></a><span class="lineno"> 639</span> <span class="preprocessor">#endif // BAMALIGNMENT_H</span></div><div class="ttc" id="_bam_aux_8h_html"><div class="ttname"><a href="_bam_aux_8h.html">BamAux.h</a></div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a5f4b4689a7898fde204f9f3275a6bcdf"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a5f4b4689a7898fde204f9f3275a6bcdf">BamTools::Constants::BAM_TAG_TYPE_FLOAT</a></div><div class="ttdeci">const char BAM_TAG_TYPE_FLOAT</div><div class="ttdef"><b>Definition:</b> BamConstants.h:80</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a9b7df792a6c644788360152e2cf56a3c"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a9b7df792a6c644788360152e2cf56a3c">BamTools::Constants::BAM_TAG_TYPE_UINT16</a></div><div class="ttdeci">const char BAM_TAG_TYPE_UINT16</div><div class="ttdef"><b>Definition:</b> BamConstants.h:77</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_aff396fa749e1439449433191eae166c7"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#aff396fa749e1439449433191eae166c7">BamTools::Constants::BAM_TAG_ARRAYBASE_SIZE</a></div><div class="ttdeci">const uint8_t BAM_TAG_ARRAYBASE_SIZE</div><div class="ttdef"><b>Definition:</b> BamConstants.h:87</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a19c45c67919fb8d22d3487b3f1fcd79d"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a19c45c67919fb8d22d3487b3f1fcd79d">BamTools::BamAlignment::InsertSize</a></div><div class="ttdeci">int32_t InsertSize</div><div class="ttdoc">mate-pair insert size </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:131</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_ab3ac5fc4c4f193d0448882e592a31962"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#ab3ac5fc4c4f193d0448882e592a31962">BamTools::BamAlignment::TagData</a></div><div class="ttdeci">std::string TagData</div><div class="ttdoc">tag data (use the provided methods to query/modify) </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:122</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a8cb4f3703011f90521564830a7f7df01"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a8cb4f3703011f90521564830a7f7df01">BamTools::Constants::BAM_TAG_TYPE_INT8</a></div><div class="ttdeci">const char BAM_TAG_TYPE_INT8</div><div class="ttdef"><b>Definition:</b> BamConstants.h:74</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="class_bam_tools_1_1_bam_alignment_html_a528e10f19aec995e58ec7dbdf1e35b6b"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a528e10f19aec995e58ec7dbdf1e35b6b">BamTools::BamAlignment::AlignmentFlag</a></div><div class="ttdeci">uint32_t AlignmentFlag</div><div class="ttdoc">alignment bit-flag (use the provided methods to query/modify) </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:127</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a20a298552510340fdc2b76c496186884"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a20a298552510340fdc2b76c496186884">BamTools::Constants::BAM_TAG_TYPE_INT32</a></div><div class="ttdeci">const char BAM_TAG_TYPE_INT32</div><div class="ttdef"><b>Definition:</b> BamConstants.h:78</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="class_bam_tools_1_1_bam_alignment_html_aa7068d3ba7704dbecb6b47ffbf6f8467"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#aa7068d3ba7704dbecb6b47ffbf6f8467">BamTools::BamAlignment::Bin</a></div><div class="ttdeci">uint16_t Bin</div><div class="ttdoc">BAM (standard) index bin number for this alignment. </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:125</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_abbac2cbd8b0508c36a6be13ab1aa53c4"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#abbac2cbd8b0508c36a6be13ab1aa53c4">BamTools::BamAlignment::Filename</a></div><div class="ttdeci">std::string Filename</div><div class="ttdoc">name of BAM file which this alignment comes from </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:132</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a53c2f04fc2e633f61e8f39264b6ad0b0"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a53c2f04fc2e633f61e8f39264b6ad0b0">BamTools::Constants::BAM_TAG_TYPE_ARRAY</a></div><div class="ttdeci">const char BAM_TAG_TYPE_ARRAY</div><div class="ttdef"><b>Definition:</b> BamConstants.h:83</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_ac7ad2244a0e268abdcdf09e97fadee3e"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#ac7ad2244a0e268abdcdf09e97fadee3e">BamTools::BamAlignment::CigarData</a></div><div class="ttdeci">std::vector< CigarOp > CigarData</div><div class="ttdoc">CIGAR operations for this alignment. </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:128</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_1_1_constants_html_a1f432cf41f5c315f8da46f302ab9cdc4"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a1f432cf41f5c315f8da46f302ab9cdc4">BamTools::Constants::BAM_TAG_TYPE_HEX</a></div><div class="ttdeci">const char BAM_TAG_TYPE_HEX</div><div class="ttdef"><b>Definition:</b> BamConstants.h:82</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a25602acbbce34e865d67d75b9966a4fc"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a25602acbbce34e865d67d75b9966a4fc">BamTools::Constants::BAM_TAG_TYPE_ASCII</a></div><div class="ttdeci">const char BAM_TAG_TYPE_ASCII</div><div class="ttdef"><b>Definition:</b> BamConstants.h:73</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_aed5682a27b7bc660d45d705e4411b3d5"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#aed5682a27b7bc660d45d705e4411b3d5">BamTools::BamAlignment::QueryBases</a></div><div class="ttdeci">std::string QueryBases</div><div class="ttdoc">&#39;original&#39; sequence (as reported from sequencing machine) </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:119</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="class_bam_tools_1_1_bam_alignment_html_a553f81130bf6e136ae8859bb89011c71"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a553f81130bf6e136ae8859bb89011c71">BamTools::BamAlignment::AddTag</a></div><div class="ttdeci">bool AddTag(const std::string &tag, const std::string &type, const T &value)</div><div class="ttdef"><b>Definition:</b> BamAlignment.h:193</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_acbfdd5b968249c9c074943b2d1fddca8"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#acbfdd5b968249c9c074943b2d1fddca8">BamTools::BamAlignment::MateRefID</a></div><div class="ttdeci">int32_t MateRefID</div><div class="ttdoc">ID number for reference sequence where alignment&#39;s mate was aligned. </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:129</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="_bam_constants_8h_html"><div class="ttname"><a href="_bam_constants_8h.html">BamConstants.h</a></div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a55d27086aca3e321cee411d43633a788"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a55d27086aca3e321cee411d43633a788">BamTools::BamAlignment::AlignedBases</a></div><div class="ttdeci">std::string AlignedBases</div><div class="ttdoc">&#39;aligned&#39; sequence (includes any indels, padding, clipping) </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:120</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_aa51e6bf07e0ec1f00072477492d31a57"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#aa51e6bf07e0ec1f00072477492d31a57">BamTools::Constants::BAM_TAG_TYPE_INT16</a></div><div class="ttdeci">const char BAM_TAG_TYPE_INT16</div><div class="ttdef"><b>Definition:</b> BamConstants.h:76</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a7f2d8fb36a83c9f0b14ec88100f69d62"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a7f2d8fb36a83c9f0b14ec88100f69d62">BamTools::Constants::BAM_TAG_TYPE_STRING</a></div><div class="ttdeci">const char BAM_TAG_TYPE_STRING</div><div class="ttdef"><b>Definition:</b> BamConstants.h:81</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a96c235eb7645c6e0fcf5da5bfb16a2aa"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a96c235eb7645c6e0fcf5da5bfb16a2aa">BamTools::BamAlignment::MapQuality</a></div><div class="ttdeci">uint16_t MapQuality</div><div class="ttdoc">mapping quality score </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:126</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_1_1_constants_html_a4d1b3e2b26a9d163336a4a83c62b86b7"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a4d1b3e2b26a9d163336a4a83c62b86b7">BamTools::Constants::BAM_TAG_TAGSIZE</a></div><div class="ttdeci">const uint8_t BAM_TAG_TAGSIZE</div><div class="ttdef"><b>Definition:</b> BamConstants.h:85</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_aaef8a38689198150d0627a51b53e6352"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#aaef8a38689198150d0627a51b53e6352">BamTools::BamAlignment::MatePosition</a></div><div class="ttdeci">int32_t MatePosition</div><div class="ttdoc">position (0-based) where alignment&#39;s mate starts </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:130</div></div>
<div class="ttc" id="namespace_bam_tools_html_a5ec8c1bc89a0c5979696a4a124fcbaeb"><div class="ttname"><a href="namespace_bam_tools.html#a5ec8c1bc89a0c5979696a4a124fcbaeb">BamTools::BamAlignmentVector</a></div><div class="ttdeci">std::vector< BamAlignment > BamAlignmentVector</div><div class="ttdef"><b>Definition:</b> BamAlignment.h:635</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a4d2ee5aeba57fdffc36e8fb9e01c4bb4"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a4d2ee5aeba57fdffc36e8fb9e01c4bb4">BamTools::BamAlignment::Length</a></div><div class="ttdeci">int32_t Length</div><div class="ttdoc">length of query sequence </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:118</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a0c4f77ed450936979e858e0703324dab"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a0c4f77ed450936979e858e0703324dab">BamTools::Constants::BAM_TAG_TYPE_UINT8</a></div><div class="ttdeci">const char BAM_TAG_TYPE_UINT8</div><div class="ttdef"><b>Definition:</b> BamConstants.h:75</div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_alignment_html_a9af49d39bda11b60eb12ed4162100fd6"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#a9af49d39bda11b60eb12ed4162100fd6">BamTools::BamAlignment::Qualities</a></div><div class="ttdeci">std::string Qualities</div><div class="ttdoc">FASTQ qualities (ASCII characters, not numeric values) </div><div class="ttdef"><b>Definition:</b> BamAlignment.h:121</div></div>
<div class="ttc" id="namespace_bam_tools_1_1_constants_html_a657c724f6561af0520aa6c2f4c23f740"><div class="ttname"><a href="namespace_bam_tools_1_1_constants.html#a657c724f6561af0520aa6c2f4c23f740">BamTools::Constants::BAM_TAG_TYPE_UINT32</a></div><div class="ttdeci">const char BAM_TAG_TYPE_UINT32</div><div class="ttdef"><b>Definition:</b> BamConstants.h:79</div></div>
<div class="ttc" id="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
<div class="ttc" id="class_bam_tools_1_1_bam_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="class_bam_tools_1_1_bam_alignment_html_af70ac92ef127712790dff1cddfb3bccd"><div class="ttname"><a href="class_bam_tools_1_1_bam_alignment.html#af70ac92ef127712790dff1cddfb3bccd">BamTools::BamAlignment::EditTag</a></div><div class="ttdeci">bool EditTag(const std::string &tag, const std::string &type, const T &value)</div><div class="ttdef"><b>Definition:</b> BamAlignment.h:372</div></div>
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