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<a href="_sam_header_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// SamHeader.h (c) 2010 Derek Barnett</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// Marth Lab, Department of Biology, Boston College</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// Last modified: 10 October 2011 (DB)</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// Provides direct read/write access to the SAM header data fields.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> </div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#ifndef SAM_HEADER_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define SAM_HEADER_H</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "<a class="code" href="api__global_8h.html">api/api_global.h</a>"</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "<a class="code" href="_bam_aux_8h.html">api/BamAux.h</a>"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include "<a class="code" href="_sam_program_chain_8h.html">api/SamProgramChain.h</a>"</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include "<a class="code" href="_sam_read_group_dictionary_8h.html">api/SamReadGroupDictionary.h</a>"</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include "<a class="code" href="_sam_sequence_dictionary_8h.html">api/SamSequenceDictionary.h</a>"</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html"> 24</a></span> <span class="keyword">struct </span><a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <a class="code" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> {</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="comment">// ctor & dtor</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <a class="code" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a>(<span class="keyword">const</span> std::string& headerText = <span class="stringliteral">""</span>);</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  SamHeader(<span class="keyword">const</span> SamHeader& other);</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  ~SamHeader(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="comment">// query/modify entire SamHeader</span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordtype">void</span> Clear(<span class="keywordtype">void</span>); <span class="comment">// clears all header contents</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  std::string GetErrorString(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordtype">bool</span> HasError(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordtype">bool</span> IsValid(<span class="keywordtype">bool</span> verbose = <span class="keyword">false</span>) <span class="keyword">const</span>; <span class="comment">// returns true if SAM header is well-formed</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordtype">void</span> SetHeaderText(<span class="keyword">const</span> std::string& headerText); <span class="comment">// replaces data fields with contents of SAM-formatted text</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  std::string ToString(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns the printable, SAM-formatted header text</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="comment">// convenience query methods</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordtype">bool</span> HasVersion(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains format version entry</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordtype">bool</span> HasSortOrder(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains sort order entry</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordtype">bool</span> HasGroupOrder(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains group order entry</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordtype">bool</span> HasSequences(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains any sequence entries</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">bool</span> HasReadGroups(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains any read group entries</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">bool</span> HasPrograms(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains any program record entries</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordtype">bool</span> HasComments(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if header contains comments</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="comment">// --------------</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="comment">// --------------</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="comment">// header metadata (@HD line)</span></div><div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#aab5d0a3271fba147105ef018587f7508"> 53</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_header.html#aab5d0a3271fba147105ef018587f7508">Version</a>; <span class="comment">// VN:<Version> *Required, if @HD record is present*</span></div><div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#a384c41739a162b4300560ec05d3538fa"> 54</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_header.html#a384c41739a162b4300560ec05d3538fa">SortOrder</a>; <span class="comment">// SO:<SortOrder></span></div><div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#a81ac2ace0ee76a2dd5d75ce0bdb499b8"> 55</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_header.html#a81ac2ace0ee76a2dd5d75ce0bdb499b8">GroupOrder</a>; <span class="comment">// GO:<GroupOrder></span></div><div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#a92cb3b3de4a559859670236fb939be94"> 56</a></span>  std::vector<CustomHeaderTag> <a class="code" href="struct_bam_tools_1_1_sam_header.html#a92cb3b3de4a559859670236fb939be94">CustomTags</a>; <span class="comment">// optional custom tags on @HD line</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="comment">// header sequences (@SQ entries)</span></div><div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#a23f21c3625ece2c3ec151f6b37cd7203"> 59</a></span>  <a class="code" href="class_bam_tools_1_1_sam_sequence_dictionary.html">SamSequenceDictionary</a> <a class="code" href="struct_bam_tools_1_1_sam_header.html#a23f21c3625ece2c3ec151f6b37cd7203">Sequences</a>;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="comment">// header read groups (@RG entries)</span></div><div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#a0de313fc16141a0b013f90c1c524ecee"> 62</a></span>  <a class="code" href="class_bam_tools_1_1_sam_read_group_dictionary.html">SamReadGroupDictionary</a> <a class="code" href="struct_bam_tools_1_1_sam_header.html#a0de313fc16141a0b013f90c1c524ecee">ReadGroups</a>;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="comment">// header program data (@PG entries)</span></div><div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#aad689b9b4dbbd211664c08f89f745b1d"> 65</a></span>  <a class="code" href="class_bam_tools_1_1_sam_program_chain.html">SamProgramChain</a> <a class="code" href="struct_bam_tools_1_1_sam_header.html#aad689b9b4dbbd211664c08f89f745b1d">Programs</a>;</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="comment">// header comments (@CO entries)</span></div><div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_header.html#a4892d51db975564d20b2df39dda4369e"> 68</a></span>  std::vector<std::string> <a class="code" href="struct_bam_tools_1_1_sam_header.html#a4892d51db975564d20b2df39dda4369e">Comments</a>;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="comment">// internal data</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">mutable</span> std::string m_errorString;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> };</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="preprocessor">#endif // SAM_HEADER_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="_sam_program_chain_8h_html"><div class="ttname"><a href="_sam_program_chain_8h.html">SamProgramChain.h</a></div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_aad689b9b4dbbd211664c08f89f745b1d"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#aad689b9b4dbbd211664c08f89f745b1d">BamTools::SamHeader::Programs</a></div><div class="ttdeci">SamProgramChain Programs</div><div class="ttdoc">corresponds to @PG entries </div><div class="ttdef"><b>Definition:</b> SamHeader.h:65</div></div>
<div class="ttc" id="_sam_read_group_dictionary_8h_html"><div class="ttname"><a href="_sam_read_group_dictionary_8h.html">SamReadGroupDictionary.h</a></div></div>
<div class="ttc" id="_sam_sequence_dictionary_8h_html"><div class="ttname"><a href="_sam_sequence_dictionary_8h.html">SamSequenceDictionary.h</a></div></div>
<div class="ttc" id="api__global_8h_html_a5e3652cae8b48c1ad174f0b06bbd06d0"><div class="ttname"><a href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a></div><div class="ttdeci">#define API_EXPORT</div><div class="ttdef"><b>Definition:</b> api_global.h:18</div></div>
<div class="ttc" id="class_bam_tools_1_1_sam_program_chain_html"><div class="ttname"><a href="class_bam_tools_1_1_sam_program_chain.html">BamTools::SamProgramChain</a></div><div class="ttdoc">Sorted container "chain" of SamProgram records. </div><div class="ttdef"><b>Definition:</b> SamProgramChain.h:26</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_aab5d0a3271fba147105ef018587f7508"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#aab5d0a3271fba147105ef018587f7508">BamTools::SamHeader::Version</a></div><div class="ttdeci">std::string Version</div><div class="ttdoc">corresponds to @HD VN:<Version> </div><div class="ttdef"><b>Definition:</b> SamHeader.h:53</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_a384c41739a162b4300560ec05d3538fa"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#a384c41739a162b4300560ec05d3538fa">BamTools::SamHeader::SortOrder</a></div><div class="ttdeci">std::string SortOrder</div><div class="ttdoc">corresponds to @HD SO:<SortOrder> </div><div class="ttdef"><b>Definition:</b> SamHeader.h:54</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_a92cb3b3de4a559859670236fb939be94"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#a92cb3b3de4a559859670236fb939be94">BamTools::SamHeader::CustomTags</a></div><div class="ttdeci">std::vector< CustomHeaderTag > CustomTags</div><div class="ttdef"><b>Definition:</b> SamHeader.h:56</div></div>
<div class="ttc" id="class_bam_tools_1_1_sam_read_group_dictionary_html"><div class="ttname"><a href="class_bam_tools_1_1_sam_read_group_dictionary.html">BamTools::SamReadGroupDictionary</a></div><div class="ttdoc">Container of SamReadGroup entries. </div><div class="ttdef"><b>Definition:</b> SamReadGroupDictionary.h:25</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html">BamTools::SamHeader</a></div><div class="ttdoc">Represents the SAM-formatted text header that is part of the BAM file header. </div><div class="ttdef"><b>Definition:</b> SamHeader.h:24</div></div>
<div class="ttc" id="class_bam_tools_1_1_sam_sequence_dictionary_html"><div class="ttname"><a href="class_bam_tools_1_1_sam_sequence_dictionary.html">BamTools::SamSequenceDictionary</a></div><div class="ttdoc">Container of SamSequence entries. </div><div class="ttdef"><b>Definition:</b> SamSequenceDictionary.h:25</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_a0de313fc16141a0b013f90c1c524ecee"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#a0de313fc16141a0b013f90c1c524ecee">BamTools::SamHeader::ReadGroups</a></div><div class="ttdeci">SamReadGroupDictionary ReadGroups</div><div class="ttdoc">corresponds to @RG entries </div><div class="ttdef"><b>Definition:</b> SamHeader.h:62</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_a4892d51db975564d20b2df39dda4369e"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#a4892d51db975564d20b2df39dda4369e">BamTools::SamHeader::Comments</a></div><div class="ttdeci">std::vector< std::string > Comments</div><div class="ttdoc">corresponds to @CO entries </div><div class="ttdef"><b>Definition:</b> SamHeader.h:68</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_a23f21c3625ece2c3ec151f6b37cd7203"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#a23f21c3625ece2c3ec151f6b37cd7203">BamTools::SamHeader::Sequences</a></div><div class="ttdeci">SamSequenceDictionary Sequences</div><div class="ttdoc">corresponds to @SQ entries </div><div class="ttdef"><b>Definition:</b> SamHeader.h:59</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_header_html_a81ac2ace0ee76a2dd5d75ce0bdb499b8"><div class="ttname"><a href="struct_bam_tools_1_1_sam_header.html#a81ac2ace0ee76a2dd5d75ce0bdb499b8">BamTools::SamHeader::GroupOrder</a></div><div class="ttdeci">std::string GroupOrder</div><div class="ttdoc">corresponds to @HD GO:<GroupOrder> </div><div class="ttdef"><b>Definition:</b> SamHeader.h:55</div></div>
<div class="ttc" id="namespace_bam_tools_html"><div class="ttname"><a href="namespace_bam_tools.html">BamTools</a></div><div class="ttdoc">Contains all BamTools classes & methods. </div><div class="ttdef"><b>Definition:</b> Sort.h:24</div></div>
<div class="ttc" id="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
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