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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>&#160;<span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">// BamAlignment.h (c) 2009 Derek Barnett</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// Marth Lab, Department of Biology, Boston College</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// Last modified: 25 July 2013 (DB)</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// Provides the BamAlignment data structure</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;</div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="preprocessor">#ifndef BAMALIGNMENT_H</span></div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#define BAMALIGNMENT_H</span></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;</div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="api__global_8h.html">api/api_global.h</a>&quot;</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_bam_aux_8h.html">api/BamAux.h</a>&quot;</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_bam_constants_8h.html">api/BamConstants.h</a>&quot;</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="preprocessor">#include &lt;cstdlib&gt;</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="preprocessor">#include &lt;cstring&gt;</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;</div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<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>&#160;</div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// forward declaration of BamAlignment&#39;s &quot;friends&quot;</span></div><div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="keyword">namespace </span>Internal {</div><div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;    <span class="keyword">class </span>BamReaderPrivate;</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;    <span class="keyword">class </span>BamWriterPrivate;</div><div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;} <span class="comment">// namespace Internal</span></div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<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>&#160;<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>&#160;</div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;    <span class="comment">// constructors &amp; destructor</span></div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;        <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>&#160;        <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>&amp; other);</div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;        ~<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>&#160;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    <span class="comment">// queries against alignment flags</span></div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="keyword">public</span>:        </div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;        <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>&#160;        <span class="keywordtype">bool</span> IsMateMapped(<span class="keywordtype">void</span>) <span class="keyword">const</span>;        <span class="comment">// returns true if alignment&#39;s mate is mapped</span></div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;        <span class="keywordtype">bool</span> IsMateReverseStrand(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if alignment&#39;s mate mapped to reverse strand</span></div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;        <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>&#160;        <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>&#160;</div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    <span class="comment">// manipulate alignment flags</span></div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    <span class="keyword">public</span>:        </div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;        <span class="keywordtype">void</span> SetIsDuplicate(<span class="keywordtype">bool</span> ok);         <span class="comment">// sets value of &quot;PCR duplicate&quot; flag</span></div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;        <span class="keywordtype">void</span> SetIsFailedQC(<span class="keywordtype">bool</span> ok);          <span class="comment">// sets value of &quot;failed quality control&quot; flag</span></div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;        <span class="keywordtype">void</span> SetIsFirstMate(<span class="keywordtype">bool</span> ok);         <span class="comment">// sets value of &quot;alignment is first mate&quot; flag</span></div><div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;        <span class="keywordtype">void</span> SetIsMapped(<span class="keywordtype">bool</span> ok);            <span class="comment">// sets value of &quot;alignment is mapped&quot; flag</span></div><div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;        <span class="keywordtype">void</span> SetIsMateMapped(<span class="keywordtype">bool</span> ok);        <span class="comment">// sets value of &quot;alignment&#39;s mate is mapped&quot; flag</span></div><div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;        <span class="keywordtype">void</span> SetIsMateReverseStrand(<span class="keywordtype">bool</span> ok); <span class="comment">// sets value of &quot;alignment&#39;s mate mapped to reverse strand&quot; flag</span></div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;        <span class="keywordtype">void</span> SetIsPaired(<span class="keywordtype">bool</span> ok);            <span class="comment">// sets value of &quot;alignment part of paired-end read&quot; flag</span></div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;        <span class="keywordtype">void</span> SetIsPrimaryAlignment(<span class="keywordtype">bool</span> ok);  <span class="comment">// sets value of &quot;position is primary alignment&quot; flag</span></div><div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;        <span class="keywordtype">void</span> SetIsProperPair(<span class="keywordtype">bool</span> ok);        <span class="comment">// sets value of &quot;alignment is part of read that satisfied paired-end resolution&quot; flag</span></div><div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;        <span class="keywordtype">void</span> SetIsReverseStrand(<span class="keywordtype">bool</span> ok);     <span class="comment">// sets value of &quot;alignment mapped to reverse strand&quot; flag</span></div><div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;        <span class="keywordtype">void</span> SetIsSecondMate(<span class="keywordtype">bool</span> ok);        <span class="comment">// sets value of &quot;alignment is second mate on read&quot; flag</span></div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="comment">// tag data access methods</span></div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;</div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;        <span class="comment">// add a new tag</span></div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt; <span class="keywordtype">bool</span> AddTag(<span class="keyword">const</span> std::string&amp; tag, <span class="keyword">const</span> std::string&amp; type, <span class="keyword">const</span> T&amp; value);</div><div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt; <span class="keywordtype">bool</span> AddTag(<span class="keyword">const</span> std::string&amp; tag, <span class="keyword">const</span> std::vector&lt;T&gt;&amp; values);</div><div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div><div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;        <span class="comment">// edit (or append) tag</span></div><div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt; <span class="keywordtype">bool</span> EditTag(<span class="keyword">const</span> std::string&amp; tag, <span class="keyword">const</span> std::string&amp; type, <span class="keyword">const</span> T&amp; value);</div><div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt; <span class="keywordtype">bool</span> EditTag(<span class="keyword">const</span> std::string&amp; tag, <span class="keyword">const</span> std::vector&lt;T&gt;&amp; values);</div><div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div><div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        <span class="comment">// retrieves tag data</span></div><div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt; <span class="keywordtype">bool</span> GetTag(<span class="keyword">const</span> std::string&amp; tag, T&amp; destination) <span class="keyword">const</span>;</div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        <span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt; <span class="keywordtype">bool</span> GetTag(<span class="keyword">const</span> std::string&amp; tag, std::vector&lt;T&gt;&amp; destination) <span class="keyword">const</span>;</div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        <span class="comment">// retrieves all current tag names</span></div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        std::vector&lt;std::string&gt; GetTagNames(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;        <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>&#160;        <span class="keywordtype">bool</span> GetTagType(<span class="keyword">const</span> std::string&amp; tag, <span class="keywordtype">char</span>&amp; type) <span class="keyword">const</span>;</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;        <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>&#160;        <span class="keywordtype">bool</span> GetArrayTagType(<span class="keyword">const</span> std::string&amp; tag, <span class="keywordtype">char</span>&amp; type) <span class="keyword">const</span>;</div><div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div><div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        <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>&#160;        <span class="keywordtype">bool</span> HasTag(<span class="keyword">const</span> std::string&amp; tag) <span class="keyword">const</span>;</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        <span class="comment">// removes a tag</span></div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;        <span class="keywordtype">void</span> RemoveTag(<span class="keyword">const</span> std::string&amp; tag);</div><div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div><div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    <span class="comment">// additional methods</span></div><div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;        <span class="comment">// populates alignment string fields</span></div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;        <span class="keywordtype">bool</span> BuildCharData(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;</div><div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        <span class="comment">// calculates alignment end position</span></div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        <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>&#160;</div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        <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>&#160;        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>&#160;</div><div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        <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>&#160;        <span class="keywordtype">bool</span> GetSoftClips(std::vector&lt;int&gt;&amp; clipSizes,</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;                          std::vector&lt;int&gt;&amp; readPositions,</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;                          std::vector&lt;int&gt;&amp; genomePositions,</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;                          <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>&#160;</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    <span class="comment">// public data fields</span></div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    <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>&#160;        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>&#160;        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>&#160;        std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#aed5682a27b7bc660d45d705e4411b3d5">QueryBases</a>;         <span class="comment">// &#39;original&#39; 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>&#160;        std::string <a class="code" href="class_bam_tools_1_1_bam_alignment.html#a55d27086aca3e321cee411d43633a788">AlignedBases</a>;       <span class="comment">// &#39;aligned&#39; 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>&#160;        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>&#160;        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>&#160;        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>&#160;        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>&#160;        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>&#160;        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>&#160;        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>&#160;        std::vector&lt;CigarOp&gt; <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>&#160;        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&#39;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>&#160;        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&#39;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>&#160;        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>&#160;        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>&#160;</div><div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;    <span class="comment">// internal utility methods</span></div><div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;    <span class="keyword">private</span>:</div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;        <span class="keywordtype">bool</span> FindTag(<span class="keyword">const</span> std::string&amp; tag,</div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;                     <span class="keywordtype">char</span>*&amp; pTagData,</div><div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;                     <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>&amp; tagDataLength,</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;                     <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>&amp; numBytesParsed) <span class="keyword">const</span>;</div><div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        <span class="keywordtype">bool</span> IsValidSize(<span class="keyword">const</span> std::string&amp; tag, <span class="keyword">const</span> std::string&amp; type) <span class="keyword">const</span>;</div><div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;        <span class="keywordtype">void</span> SetErrorString(<span class="keyword">const</span> std::string&amp; where, <span class="keyword">const</span> std::string&amp; what) <span class="keyword">const</span>;</div><div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        <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>&#160;                           <span class="keywordtype">char</span>*&amp; pTagData,</div><div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;                           <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>&amp; numBytesParsed) <span class="keyword">const</span>;</div><div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;    <span class="comment">// internal data</span></div><div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;    <span class="keyword">private</span>:</div><div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;</div><div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;        <span class="keyword">struct </span>BamAlignmentSupportData {</div><div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;</div><div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;            <span class="comment">// data members</span></div><div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;            std::string AllCharData;</div><div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;            uint32_t    BlockLength;</div><div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;            uint32_t    NumCigarOperations;</div><div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;            uint32_t    QueryNameLength;</div><div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;            uint32_t    QuerySequenceLength;</div><div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;            <span class="keywordtype">bool</span>        HasCoreOnly;</div><div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div><div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;            <span class="comment">// constructor</span></div><div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;            BamAlignmentSupportData(<span class="keywordtype">void</span>)</div><div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;                : BlockLength(0)</div><div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;                , NumCigarOperations(0)</div><div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;                , QueryNameLength(0)</div><div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;                , QuerySequenceLength(0)</div><div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;                , HasCoreOnly(false)</div><div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            { }</div><div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        };</div><div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;        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>&#160;        <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>&#160;        <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>&#160;</div><div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;        <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>&#160;};</div><div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;</div><div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;<span class="comment">// ---------------------------------------------------------</span></div><div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;<span class="comment">// BamAlignment tag access methods</span></div><div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;</div><div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt;</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>&#160;<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&amp; tag, <span class="keyword">const</span> std::string&amp; type, <span class="keyword">const</span> T&amp; value) {</div><div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div><div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;        BuildCharData();</div><div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;</div><div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;    <span class="comment">// check tag/type size</span></div><div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    <span class="keywordflow">if</span> ( !IsValidSize(tag, type) ) {</div><div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    }</div><div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;</div><div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( !TagTypeHelper&lt;T&gt;::CanConvertTo(type.at(0)) ) {</div><div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;    }</div><div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div><div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;    <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;    <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>&#160;    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    <span class="comment">// if tag already exists, return false</span></div><div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;    <span class="comment">// use EditTag explicitly instead</span></div><div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;    <span class="keywordflow">if</span> ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;    }</div><div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;</div><div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;    <span class="comment">// otherwise, convert value to string</span></div><div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;    <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>&#160;    un.value = value;</div><div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;</div><div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;    <span class="comment">// copy original tag data to temp buffer</span></div><div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;    <span class="keyword">const</span> std::string newTag = tag + type;</div><div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;    <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>&#160;    RaiiBuffer originalTagData(newTagDataLength);</div><div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;    memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength + 1);    <span class="comment">// &#39;+1&#39; for TagData null-term</span></div><div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div><div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;    <span class="comment">// append newTag</span></div><div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;    strcat(originalTagData.Buffer + tagDataLength, newTag.data());</div><div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;    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>&#160;</div><div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;    <span class="comment">// store temp buffer back in TagData</span></div><div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;    <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>&#160;    TagData.assign(newTagData, newTagDataLength);</div><div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;    <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;}</div><div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div><div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;<span class="keyword">template</span>&lt;&gt;</div><div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ac9a7f11b4033e3f29183dce30e29b7da">  244</a></span>&#160;<span class="keyword">inline</span> <span class="keywordtype">bool</span> BamAlignment::AddTag&lt;std::string&gt;(<span class="keyword">const</span> std::string&amp; tag,</div><div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;                                              <span class="keyword">const</span> std::string&amp; type,</div><div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;                                              <span class="keyword">const</span> std::string&amp; value)</div><div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;{</div><div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;        BuildCharData();</div><div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;</div><div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;    <span class="comment">// check tag/type size</span></div><div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;    <span class="keywordflow">if</span> ( !IsValidSize(tag, type) ) {</div><div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;    }</div><div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;</div><div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( !TagTypeHelper&lt;std::string&gt;::CanConvertTo(type.at(0)) ) {</div><div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;    }</div><div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;</div><div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;    <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;    <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>&#160;    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;    <span class="comment">// if tag already exists, return false</span></div><div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;    <span class="comment">// use EditTag explicitly instead</span></div><div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;    <span class="keywordflow">if</span> ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;    }</div><div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;</div><div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;    <span class="comment">// otherwise, copy tag data to temp buffer</span></div><div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;    <span class="keyword">const</span> std::string newTag = tag + type + value;</div><div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;    <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>&#160;    RaiiBuffer originalTagData(newTagDataLength);</div><div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;    memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength + 1);    <span class="comment">// &#39;+1&#39; for TagData null-term</span></div><div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;</div><div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;    <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>&#160;    strcat(originalTagData.Buffer + tagDataLength, newTag.data());</div><div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;</div><div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;    <span class="comment">// store temp buffer back in TagData</span></div><div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;    <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>&#160;    TagData.assign(newTagData, newTagDataLength);</div><div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;    <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;}</div><div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;</div><div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt;</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>&#160;<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&amp; tag, <span class="keyword">const</span> std::vector&lt;T&gt;&amp; values) {</div><div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;</div><div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;        BuildCharData();</div><div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;</div><div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;    <span class="comment">// check for valid tag name length</span></div><div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;    <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>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;</div><div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;    <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;    <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>&#160;    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;    <span class="comment">// if tag already exists, return false</span></div><div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;    <span class="comment">// use EditTag explicitly instead</span></div><div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;    <span class="keywordflow">if</span> ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;    }</div><div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;</div><div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;    <span class="comment">// build new tag&#39;s base information</span></div><div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;    <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>&#160;    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>&#160;    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>&#160;    newTagBase[3] = TagTypeHelper&lt;T&gt;::TypeCode();</div><div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;</div><div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;    <span class="comment">// add number of array elements to newTagBase</span></div><div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;    <span class="keyword">const</span> int32_t numElements  = values.size();</div><div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;    memcpy(newTagBase + 4, &amp;numElements, <span class="keyword">sizeof</span>(int32_t));</div><div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;</div><div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;    <span class="comment">// copy current TagData string to temp buffer, leaving room for new tag&#39;s contents</span></div><div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;    <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>&#160;                                    <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>&#160;                                    numElements*<span class="keyword">sizeof</span>(T);</div><div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;    RaiiBuffer originalTagData(newTagDataLength);</div><div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;    memcpy(originalTagData.Buffer, TagData.c_str(), tagDataLength+1); <span class="comment">// &#39;+1&#39; for TagData&#39;s null-term</span></div><div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;</div><div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;    <span class="comment">// write newTagBase (removes old null term)</span></div><div class="line"><a name="l00342"></a><span class="lineno">  342</span>&#160;    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>&#160;</div><div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;    <span class="comment">// add vector elements to tag</span></div><div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;    <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>&#160;    <span class="keywordflow">for</span> ( <span class="keywordtype">int</span> i = 0 ; i &lt; numElements; ++i ) {</div><div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;        <span class="keyword">const</span> T&amp; value = values.at(i);</div><div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;        memcpy(originalTagData.Buffer + elementsBeginOffset + i*<span class="keyword">sizeof</span>(T), &amp;value, <span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00349"></a><span class="lineno">  349</span>&#160;    }</div><div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;</div><div class="line"><a name="l00351"></a><span class="lineno">  351</span>&#160;    <span class="comment">// store temp buffer back in TagData</span></div><div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;    <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>&#160;    TagData.assign(newTagData, newTagDataLength);</div><div class="line"><a name="l00354"></a><span class="lineno">  354</span>&#160;    <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00355"></a><span class="lineno">  355</span>&#160;}</div><div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;</div><div class="line"><a name="l00371"></a><span class="lineno">  371</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt;</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>&#160;<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&amp; tag, <span class="keyword">const</span> std::string&amp; type, <span class="keyword">const</span> T&amp; value) {</div><div class="line"><a name="l00373"></a><span class="lineno">  373</span>&#160;</div><div class="line"><a name="l00374"></a><span class="lineno">  374</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;        BuildCharData();</div><div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;</div><div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( HasTag(tag) )</div><div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;        RemoveTag(tag);</div><div class="line"><a name="l00381"></a><span class="lineno">  381</span>&#160;    <span class="keywordflow">return</span> AddTag(tag, type, value);</div><div class="line"><a name="l00382"></a><span class="lineno">  382</span>&#160;}</div><div class="line"><a name="l00383"></a><span class="lineno">  383</span>&#160;</div><div class="line"><a name="l00395"></a><span class="lineno">  395</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt;</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>&#160;<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&amp; tag, <span class="keyword">const</span> std::vector&lt;T&gt;&amp; values) {</div><div class="line"><a name="l00397"></a><span class="lineno">  397</span>&#160;</div><div class="line"><a name="l00398"></a><span class="lineno">  398</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly )</div><div class="line"><a name="l00400"></a><span class="lineno">  400</span>&#160;        BuildCharData();</div><div class="line"><a name="l00401"></a><span class="lineno">  401</span>&#160;</div><div class="line"><a name="l00402"></a><span class="lineno">  402</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( HasTag(tag) )</div><div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;        RemoveTag(tag);</div><div class="line"><a name="l00405"></a><span class="lineno">  405</span>&#160;    <span class="keywordflow">return</span> AddTag(tag, values);</div><div class="line"><a name="l00406"></a><span class="lineno">  406</span>&#160;}</div><div class="line"><a name="l00407"></a><span class="lineno">  407</span>&#160;</div><div class="line"><a name="l00408"></a><span class="lineno">  408</span>&#160;</div><div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt;</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>&#160;<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&amp; tag, T&amp; destination)<span class="keyword"> const </span>{</div><div class="line"><a name="l00418"></a><span class="lineno">  418</span>&#160;</div><div class="line"><a name="l00419"></a><span class="lineno">  419</span>&#160;    <span class="comment">// skip if alignment is core-only</span></div><div class="line"><a name="l00420"></a><span class="lineno">  420</span>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly ) {</div><div class="line"><a name="l00421"></a><span class="lineno">  421</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00422"></a><span class="lineno">  422</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00423"></a><span class="lineno">  423</span>&#160;    }</div><div class="line"><a name="l00424"></a><span class="lineno">  424</span>&#160;</div><div class="line"><a name="l00425"></a><span class="lineno">  425</span>&#160;    <span class="comment">// skip if no tags present</span></div><div class="line"><a name="l00426"></a><span class="lineno">  426</span>&#160;    <span class="keywordflow">if</span> ( TagData.empty() ) {</div><div class="line"><a name="l00427"></a><span class="lineno">  427</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00428"></a><span class="lineno">  428</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00429"></a><span class="lineno">  429</span>&#160;    }</div><div class="line"><a name="l00430"></a><span class="lineno">  430</span>&#160;</div><div class="line"><a name="l00431"></a><span class="lineno">  431</span>&#160;    <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00432"></a><span class="lineno">  432</span>&#160;    <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>&#160;    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00436"></a><span class="lineno">  436</span>&#160;    <span class="comment">// return failure if tag not found</span></div><div class="line"><a name="l00437"></a><span class="lineno">  437</span>&#160;    <span class="keywordflow">if</span> ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00438"></a><span class="lineno">  438</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00439"></a><span class="lineno">  439</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00440"></a><span class="lineno">  440</span>&#160;    }</div><div class="line"><a name="l00441"></a><span class="lineno">  441</span>&#160;</div><div class="line"><a name="l00442"></a><span class="lineno">  442</span>&#160;    <span class="comment">// fetch data type</span></div><div class="line"><a name="l00443"></a><span class="lineno">  443</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( !TagTypeHelper&lt;T&gt;::CanConvertFrom(type) ) {</div><div class="line"><a name="l00445"></a><span class="lineno">  445</span>&#160;        <span class="comment">// TODO: set error string ?</span></div><div class="line"><a name="l00446"></a><span class="lineno">  446</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00447"></a><span class="lineno">  447</span>&#160;    }</div><div class="line"><a name="l00448"></a><span class="lineno">  448</span>&#160;</div><div class="line"><a name="l00449"></a><span class="lineno">  449</span>&#160;    <span class="comment">// determine data length</span></div><div class="line"><a name="l00450"></a><span class="lineno">  450</span>&#160;    <span class="keywordtype">int</span> destinationLength = 0;</div><div class="line"><a name="l00451"></a><span class="lineno">  451</span>&#160;    <span class="keywordflow">switch</span> ( type ) {</div><div class="line"><a name="l00452"></a><span class="lineno">  452</span>&#160;</div><div class="line"><a name="l00453"></a><span class="lineno">  453</span>&#160;        <span class="comment">// 1 byte data</span></div><div class="line"><a name="l00454"></a><span class="lineno">  454</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;            destinationLength = 1;</div><div class="line"><a name="l00458"></a><span class="lineno">  458</span>&#160;            <span class="keywordflow">break</span>;</div><div class="line"><a name="l00459"></a><span class="lineno">  459</span>&#160;</div><div class="line"><a name="l00460"></a><span class="lineno">  460</span>&#160;        <span class="comment">// 2 byte data</span></div><div class="line"><a name="l00461"></a><span class="lineno">  461</span>&#160;        <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>&#160;        <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>&#160;            destinationLength = 2;</div><div class="line"><a name="l00464"></a><span class="lineno">  464</span>&#160;            <span class="keywordflow">break</span>;</div><div class="line"><a name="l00465"></a><span class="lineno">  465</span>&#160;</div><div class="line"><a name="l00466"></a><span class="lineno">  466</span>&#160;        <span class="comment">// 4 byte data</span></div><div class="line"><a name="l00467"></a><span class="lineno">  467</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;            destinationLength = 4;</div><div class="line"><a name="l00471"></a><span class="lineno">  471</span>&#160;            <span class="keywordflow">break</span>;</div><div class="line"><a name="l00472"></a><span class="lineno">  472</span>&#160;</div><div class="line"><a name="l00473"></a><span class="lineno">  473</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;        <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>&#160;            SetErrorString(<span class="stringliteral">&quot;BamAlignment::GetTag&quot;</span>,</div><div class="line"><a name="l00478"></a><span class="lineno">  478</span>&#160;                           <span class="stringliteral">&quot;cannot store variable length tag data into a numeric destination&quot;</span>);</div><div class="line"><a name="l00479"></a><span class="lineno">  479</span>&#160;            <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00480"></a><span class="lineno">  480</span>&#160;</div><div class="line"><a name="l00481"></a><span class="lineno">  481</span>&#160;        <span class="comment">// unrecognized tag type</span></div><div class="line"><a name="l00482"></a><span class="lineno">  482</span>&#160;        <span class="keywordflow">default</span>:</div><div class="line"><a name="l00483"></a><span class="lineno">  483</span>&#160;            <span class="keyword">const</span> std::string message = std::string(<span class="stringliteral">&quot;invalid tag type: &quot;</span>) + type;</div><div class="line"><a name="l00484"></a><span class="lineno">  484</span>&#160;            SetErrorString(<span class="stringliteral">&quot;BamAlignment::GetTag&quot;</span>, message);</div><div class="line"><a name="l00485"></a><span class="lineno">  485</span>&#160;            <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00486"></a><span class="lineno">  486</span>&#160;    }</div><div class="line"><a name="l00487"></a><span class="lineno">  487</span>&#160;</div><div class="line"><a name="l00488"></a><span class="lineno">  488</span>&#160;    <span class="comment">// store data in destination</span></div><div class="line"><a name="l00489"></a><span class="lineno">  489</span>&#160;    destination = 0;</div><div class="line"><a name="l00490"></a><span class="lineno">  490</span>&#160;    memcpy(&amp;destination, pTagData, destinationLength);</div><div class="line"><a name="l00491"></a><span class="lineno">  491</span>&#160;</div><div class="line"><a name="l00492"></a><span class="lineno">  492</span>&#160;    <span class="comment">// return success</span></div><div class="line"><a name="l00493"></a><span class="lineno">  493</span>&#160;    <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00494"></a><span class="lineno">  494</span>&#160;}</div><div class="line"><a name="l00495"></a><span class="lineno">  495</span>&#160;</div><div class="line"><a name="l00496"></a><span class="lineno">  496</span>&#160;<span class="keyword">template</span>&lt;&gt;</div><div class="line"><a name="l00497"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a8b6c0f9db6f33bd8213304ce47a7e857">  497</a></span>&#160;<span class="keyword">inline</span> <span class="keywordtype">bool</span> BamAlignment::GetTag&lt;std::string&gt;(<span class="keyword">const</span> std::string&amp; tag,</div><div class="line"><a name="l00498"></a><span class="lineno">  498</span>&#160;                                              std::string&amp; destination) <span class="keyword">const</span></div><div class="line"><a name="l00499"></a><span class="lineno">  499</span>&#160;{</div><div class="line"><a name="l00500"></a><span class="lineno">  500</span>&#160;    <span class="comment">// skip if alignment is core-only</span></div><div class="line"><a name="l00501"></a><span class="lineno">  501</span>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly ) {</div><div class="line"><a name="l00502"></a><span class="lineno">  502</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00503"></a><span class="lineno">  503</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00504"></a><span class="lineno">  504</span>&#160;    }</div><div class="line"><a name="l00505"></a><span class="lineno">  505</span>&#160;</div><div class="line"><a name="l00506"></a><span class="lineno">  506</span>&#160;    <span class="comment">// skip if no tags present</span></div><div class="line"><a name="l00507"></a><span class="lineno">  507</span>&#160;    <span class="keywordflow">if</span> ( TagData.empty() ) {</div><div class="line"><a name="l00508"></a><span class="lineno">  508</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00509"></a><span class="lineno">  509</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00510"></a><span class="lineno">  510</span>&#160;    }</div><div class="line"><a name="l00511"></a><span class="lineno">  511</span>&#160;</div><div class="line"><a name="l00512"></a><span class="lineno">  512</span>&#160;    <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00513"></a><span class="lineno">  513</span>&#160;    <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>&#160;    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00517"></a><span class="lineno">  517</span>&#160;    <span class="comment">// return failure if tag not found</span></div><div class="line"><a name="l00518"></a><span class="lineno">  518</span>&#160;    <span class="keywordflow">if</span> ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00519"></a><span class="lineno">  519</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00520"></a><span class="lineno">  520</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00521"></a><span class="lineno">  521</span>&#160;    }</div><div class="line"><a name="l00522"></a><span class="lineno">  522</span>&#160;</div><div class="line"><a name="l00523"></a><span class="lineno">  523</span>&#160;    <span class="comment">// otherwise copy data into destination</span></div><div class="line"><a name="l00524"></a><span class="lineno">  524</span>&#160;    <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>&#160;    destination.clear();</div><div class="line"><a name="l00526"></a><span class="lineno">  526</span>&#160;    destination.resize(dataLength);</div><div class="line"><a name="l00527"></a><span class="lineno">  527</span>&#160;    memcpy( (<span class="keywordtype">char</span>*)destination.data(), pTagData, dataLength );</div><div class="line"><a name="l00528"></a><span class="lineno">  528</span>&#160;</div><div class="line"><a name="l00529"></a><span class="lineno">  529</span>&#160;    <span class="comment">// return success</span></div><div class="line"><a name="l00530"></a><span class="lineno">  530</span>&#160;    <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00531"></a><span class="lineno">  531</span>&#160;}</div><div class="line"><a name="l00532"></a><span class="lineno">  532</span>&#160;</div><div class="line"><a name="l00540"></a><span class="lineno">  540</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> T&gt;</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>&#160;<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&amp; tag, std::vector&lt;T&gt;&amp; destination)<span class="keyword"> const </span>{</div><div class="line"><a name="l00542"></a><span class="lineno">  542</span>&#160;</div><div class="line"><a name="l00543"></a><span class="lineno">  543</span>&#160;    <span class="comment">// skip if alignment is core-only</span></div><div class="line"><a name="l00544"></a><span class="lineno">  544</span>&#160;    <span class="keywordflow">if</span> ( SupportData.HasCoreOnly ) {</div><div class="line"><a name="l00545"></a><span class="lineno">  545</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00546"></a><span class="lineno">  546</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00547"></a><span class="lineno">  547</span>&#160;    }</div><div class="line"><a name="l00548"></a><span class="lineno">  548</span>&#160;</div><div class="line"><a name="l00549"></a><span class="lineno">  549</span>&#160;    <span class="comment">// skip if no tags present</span></div><div class="line"><a name="l00550"></a><span class="lineno">  550</span>&#160;    <span class="keywordflow">if</span> ( TagData.empty() ) {</div><div class="line"><a name="l00551"></a><span class="lineno">  551</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00552"></a><span class="lineno">  552</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00553"></a><span class="lineno">  553</span>&#160;    }</div><div class="line"><a name="l00554"></a><span class="lineno">  554</span>&#160;</div><div class="line"><a name="l00555"></a><span class="lineno">  555</span>&#160;    <span class="comment">// localize the tag data</span></div><div class="line"><a name="l00556"></a><span class="lineno">  556</span>&#160;    <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>&#160;    <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>&#160;    <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>&#160;</div><div class="line"><a name="l00560"></a><span class="lineno">  560</span>&#160;    <span class="comment">// return false if tag not found</span></div><div class="line"><a name="l00561"></a><span class="lineno">  561</span>&#160;    <span class="keywordflow">if</span> ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {</div><div class="line"><a name="l00562"></a><span class="lineno">  562</span>&#160;        <span class="comment">// TODO: set error string?</span></div><div class="line"><a name="l00563"></a><span class="lineno">  563</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00564"></a><span class="lineno">  564</span>&#160;    }</div><div class="line"><a name="l00565"></a><span class="lineno">  565</span>&#160;</div><div class="line"><a name="l00566"></a><span class="lineno">  566</span>&#160;    <span class="comment">// check that tag is array type</span></div><div class="line"><a name="l00567"></a><span class="lineno">  567</span>&#160;    <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>&#160;    <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>&#160;        SetErrorString(<span class="stringliteral">&quot;BamAlignment::GetTag&quot;</span>, <span class="stringliteral">&quot;cannot store a non-array tag in array destination&quot;</span>);</div><div class="line"><a name="l00570"></a><span class="lineno">  570</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00571"></a><span class="lineno">  571</span>&#160;    }</div><div class="line"><a name="l00572"></a><span class="lineno">  572</span>&#160;</div><div class="line"><a name="l00573"></a><span class="lineno">  573</span>&#160;    <span class="comment">// fetch element type</span></div><div class="line"><a name="l00574"></a><span class="lineno">  574</span>&#160;    <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>&#160;    <span class="keywordflow">if</span> ( !TagTypeHelper&lt;T&gt;::CanConvertFrom(elementType) ) {</div><div class="line"><a name="l00576"></a><span class="lineno">  576</span>&#160;        <span class="comment">// TODO: set error string ?</span></div><div class="line"><a name="l00577"></a><span class="lineno">  577</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00578"></a><span class="lineno">  578</span>&#160;    }</div><div class="line"><a name="l00579"></a><span class="lineno">  579</span>&#160;    ++pTagData;</div><div class="line"><a name="l00580"></a><span class="lineno">  580</span>&#160;</div><div class="line"><a name="l00581"></a><span class="lineno">  581</span>&#160;    <span class="comment">// calculate length of each element in tag&#39;s array</span></div><div class="line"><a name="l00582"></a><span class="lineno">  582</span>&#160;    <span class="keywordtype">int</span> elementLength = 0;</div><div class="line"><a name="l00583"></a><span class="lineno">  583</span>&#160;    <span class="keywordflow">switch</span> ( elementType ) {</div><div class="line"><a name="l00584"></a><span class="lineno">  584</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;            elementLength = <span class="keyword">sizeof</span>(uint8_t);</div><div class="line"><a name="l00588"></a><span class="lineno">  588</span>&#160;            <span class="keywordflow">break</span>;</div><div class="line"><a name="l00589"></a><span class="lineno">  589</span>&#160;</div><div class="line"><a name="l00590"></a><span class="lineno">  590</span>&#160;        <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>&#160;        <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>&#160;            elementLength = <span class="keyword">sizeof</span>(uint16_t);</div><div class="line"><a name="l00593"></a><span class="lineno">  593</span>&#160;            <span class="keywordflow">break</span>;</div><div class="line"><a name="l00594"></a><span class="lineno">  594</span>&#160;</div><div class="line"><a name="l00595"></a><span class="lineno">  595</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;            elementLength = <span class="keyword">sizeof</span>(uint32_t);</div><div class="line"><a name="l00599"></a><span class="lineno">  599</span>&#160;            <span class="keywordflow">break</span>;</div><div class="line"><a name="l00600"></a><span class="lineno">  600</span>&#160;</div><div class="line"><a name="l00601"></a><span class="lineno">  601</span>&#160;        <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>&#160;        <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>&#160;        <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>&#160;        <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>&#160;            SetErrorString(<span class="stringliteral">&quot;BamAlignment::GetTag&quot;</span>,</div><div class="line"><a name="l00606"></a><span class="lineno">  606</span>&#160;                           <span class="stringliteral">&quot;invalid array data, variable-length elements are not allowed&quot;</span>);</div><div class="line"><a name="l00607"></a><span class="lineno">  607</span>&#160;            <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00608"></a><span class="lineno">  608</span>&#160;</div><div class="line"><a name="l00609"></a><span class="lineno">  609</span>&#160;        <span class="comment">// unknown tag type</span></div><div class="line"><a name="l00610"></a><span class="lineno">  610</span>&#160;        <span class="keywordflow">default</span>:</div><div class="line"><a name="l00611"></a><span class="lineno">  611</span>&#160;            <span class="keyword">const</span> std::string message = std::string(<span class="stringliteral">&quot;invalid array element type: &quot;</span>) + elementType;</div><div class="line"><a name="l00612"></a><span class="lineno">  612</span>&#160;            SetErrorString(<span class="stringliteral">&quot;BamAlignment::GetTag&quot;</span>, message);</div><div class="line"><a name="l00613"></a><span class="lineno">  613</span>&#160;            <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00614"></a><span class="lineno">  614</span>&#160;    }</div><div class="line"><a name="l00615"></a><span class="lineno">  615</span>&#160;</div><div class="line"><a name="l00616"></a><span class="lineno">  616</span>&#160;    <span class="comment">// get number of elements</span></div><div class="line"><a name="l00617"></a><span class="lineno">  617</span>&#160;    int32_t numElements;</div><div class="line"><a name="l00618"></a><span class="lineno">  618</span>&#160;    memcpy(&amp;numElements, pTagData, <span class="keyword">sizeof</span>(int32_t));</div><div class="line"><a name="l00619"></a><span class="lineno">  619</span>&#160;    pTagData += 4;</div><div class="line"><a name="l00620"></a><span class="lineno">  620</span>&#160;    destination.clear();</div><div class="line"><a name="l00621"></a><span class="lineno">  621</span>&#160;    destination.reserve(numElements);</div><div class="line"><a name="l00622"></a><span class="lineno">  622</span>&#160;</div><div class="line"><a name="l00623"></a><span class="lineno">  623</span>&#160;    <span class="comment">// read in elements</span></div><div class="line"><a name="l00624"></a><span class="lineno">  624</span>&#160;    T value;</div><div class="line"><a name="l00625"></a><span class="lineno">  625</span>&#160;    <span class="keywordflow">for</span> ( <span class="keywordtype">int</span> i = 0 ; i &lt; numElements; ++i ) {</div><div class="line"><a name="l00626"></a><span class="lineno">  626</span>&#160;        memcpy(&amp;value, pTagData, <span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00627"></a><span class="lineno">  627</span>&#160;        pTagData += <span class="keyword">sizeof</span>(T);</div><div class="line"><a name="l00628"></a><span class="lineno">  628</span>&#160;        destination.push_back(value);</div><div class="line"><a name="l00629"></a><span class="lineno">  629</span>&#160;    }</div><div class="line"><a name="l00630"></a><span class="lineno">  630</span>&#160;</div><div class="line"><a name="l00631"></a><span class="lineno">  631</span>&#160;    <span class="comment">// return success</span></div><div class="line"><a name="l00632"></a><span class="lineno">  632</span>&#160;    <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00633"></a><span class="lineno">  633</span>&#160;}</div><div class="line"><a name="l00634"></a><span class="lineno">  634</span>&#160;</div><div class="line"><a name="l00635"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#a5ec8c1bc89a0c5979696a4a124fcbaeb">  635</a></span>&#160;<span class="keyword">typedef</span> std::vector&lt;BamAlignment&gt; <a class="code" href="namespace_bam_tools.html#a5ec8c1bc89a0c5979696a4a124fcbaeb">BamAlignmentVector</a>;</div><div class="line"><a name="l00636"></a><span class="lineno">  636</span>&#160;</div><div class="line"><a name="l00637"></a><span class="lineno">  637</span>&#160;} <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00638"></a><span class="lineno">  638</span>&#160;</div><div class="line"><a name="l00639"></a><span class="lineno">  639</span>&#160;<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 &amp;tag, T &amp;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&lt; CigarOp &gt; 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">&amp;#39;original&amp;#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 &amp;tag, const std::string &amp;type, const T &amp;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&amp;#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">&amp;#39;aligned&amp;#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 &amp; 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&amp;#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&lt; BamAlignment &gt; 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 &amp;tag, const std::string &amp;type, const T &amp;value)</div><div class="ttdef"><b>Definition:</b> BamAlignment.h:372</div></div>
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