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<a href="_sam_program_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">// SamProgram.h (c) 2011 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 program records.</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_PROGRAM_H</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#define SAM_PROGRAM_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 <string></span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">class </span>SamProgramChain;</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html"> 21</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_program.html">SamProgram</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>  <span class="comment">// ctor & dtor</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <a class="code" href="struct_bam_tools_1_1_sam_program.html">SamProgram</a>(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  SamProgram(<span class="keyword">const</span> std::string& <span class="keywordtype">id</span>);</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  SamProgram(<span class="keyword">const</span> SamProgram& other);</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  ~SamProgram(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="comment">// query/modify entire program record</span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">void</span> Clear(<span class="keywordtype">void</span>); <span class="comment">// clears all data fields</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="comment">// convenience query methods</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordtype">bool</span> HasCommandLine(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if program record has a command line entry</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordtype">bool</span> HasID(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if program record has an ID</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordtype">bool</span> HasName(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if program record has a name</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordtype">bool</span> HasPreviousProgramID(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if program record has a 'previous program ID'</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordtype">bool</span> HasVersion(<span class="keywordtype">void</span>) <span class="keyword">const</span>; <span class="comment">// returns true if program record has a version</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">// data members</span></div><div class="line"><a name="l00040"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#ad1754d9c2a563f5ad3db72b84e42d03d"> 40</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_program.html#ad1754d9c2a563f5ad3db72b84e42d03d">CommandLine</a>; <span class="comment">// CL:<CommandLine></span></div><div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#ae589e95036e7163e7363593de540d340"> 41</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_program.html#ae589e95036e7163e7363593de540d340">ID</a>; <span class="comment">// ID:<ID> *Required for valid SAM header*</span></div><div class="line"><a name="l00042"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#a1db41b0088eaf6d97477fa3f6104c40a"> 42</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_program.html#a1db41b0088eaf6d97477fa3f6104c40a">Name</a>; <span class="comment">// PN:<Name></span></div><div class="line"><a name="l00043"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#a7890f0688e0da803c272d7dfa0c3fd0c"> 43</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_program.html#a7890f0688e0da803c272d7dfa0c3fd0c">PreviousProgramID</a>; <span class="comment">// PP:<PreviousProgramID></span></div><div class="line"><a name="l00044"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#a672d66422c5304713d07a53e4701ccae"> 44</a></span>  std::string <a class="code" href="struct_bam_tools_1_1_sam_program.html#a672d66422c5304713d07a53e4701ccae">Version</a>; <span class="comment">// VN:<Version></span></div><div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#a5733e84e40aaf9c1b4c12c538bb23a8a"> 45</a></span>  std::vector<CustomHeaderTag> <a class="code" href="struct_bam_tools_1_1_sam_program.html#a5733e84e40aaf9c1b4c12c538bb23a8a">CustomTags</a>; <span class="comment">// optional custom tags</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="comment">// internal (non-standard) methods & fields</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">private</span>:</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">bool</span> HasNextProgramID(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  std::string NextProgramID;</div><div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="struct_bam_tools_1_1_sam_program.html#abdba35c7be88b6e26d45de5938d0cce3"> 51</a></span>  <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="class_bam_tools_1_1_sam_program_chain.html">BamTools::SamProgramChain</a>;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> };</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="namespace_bam_tools.html#ada5374e28a46d3d386a7d3e22af41574"> 57</a></span> <a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="namespace_bam_tools.html#ada5374e28a46d3d386a7d3e22af41574">operator==</a>(<span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_sam_program.html">SamProgram</a>& lhs, <span class="keyword">const</span> <a class="code" href="struct_bam_tools_1_1_sam_program.html">SamProgram</a>& rhs) {</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">return</span> lhs.<a class="code" href="struct_bam_tools_1_1_sam_program.html#ae589e95036e7163e7363593de540d340">ID</a> == rhs.<a class="code" href="struct_bam_tools_1_1_sam_program.html#ae589e95036e7163e7363593de540d340">ID</a>;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> }</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">// namespace BamTools</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="preprocessor">#endif // SAM_PROGRAM_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="struct_bam_tools_1_1_sam_program_html_a5733e84e40aaf9c1b4c12c538bb23a8a"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html#a5733e84e40aaf9c1b4c12c538bb23a8a">BamTools::SamProgram::CustomTags</a></div><div class="ttdeci">std::vector< CustomHeaderTag > CustomTags</div><div class="ttdef"><b>Definition:</b> SamProgram.h:45</div></div>
<div class="ttc" id="namespace_bam_tools_html_ada5374e28a46d3d386a7d3e22af41574"><div class="ttname"><a href="namespace_bam_tools.html#ada5374e28a46d3d386a7d3e22af41574">BamTools::operator==</a></div><div class="ttdeci">API_EXPORT bool operator==(const SamProgram &lhs, const SamProgram &rhs)</div><div class="ttdoc">tests equality by comparing program IDs </div><div class="ttdef"><b>Definition:</b> SamProgram.h:57</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_program_html_a7890f0688e0da803c272d7dfa0c3fd0c"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html#a7890f0688e0da803c272d7dfa0c3fd0c">BamTools::SamProgram::PreviousProgramID</a></div><div class="ttdeci">std::string PreviousProgramID</div><div class="ttdoc">corresponds to @PG PP:<PreviousProgramID> </div><div class="ttdef"><b>Definition:</b> SamProgram.h:43</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_program_html_a1db41b0088eaf6d97477fa3f6104c40a"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html#a1db41b0088eaf6d97477fa3f6104c40a">BamTools::SamProgram::Name</a></div><div class="ttdeci">std::string Name</div><div class="ttdoc">corresponds to @PG PN:<Name> </div><div class="ttdef"><b>Definition:</b> SamProgram.h:42</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_program_html_a672d66422c5304713d07a53e4701ccae"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html#a672d66422c5304713d07a53e4701ccae">BamTools::SamProgram::Version</a></div><div class="ttdeci">std::string Version</div><div class="ttdoc">corresponds to @PG VN:<Version> </div><div class="ttdef"><b>Definition:</b> SamProgram.h:44</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_program_html_ae589e95036e7163e7363593de540d340"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html#ae589e95036e7163e7363593de540d340">BamTools::SamProgram::ID</a></div><div class="ttdeci">std::string ID</div><div class="ttdoc">corresponds to @PG ID:<ID> </div><div class="ttdef"><b>Definition:</b> SamProgram.h:41</div></div>
<div class="ttc" id="namespace_bam_tools_html"><div class="ttname"><a href="namespace_bam_tools.html">BamTools</a></div><div class="ttdoc">Contains all BamTools classes & methods. </div><div class="ttdef"><b>Definition:</b> Sort.h:24</div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_program_html"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html">BamTools::SamProgram</a></div><div class="ttdoc">Represents a SAM program record. </div><div class="ttdef"><b>Definition:</b> SamProgram.h:21</div></div>
<div class="ttc" id="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
<div class="ttc" id="struct_bam_tools_1_1_sam_program_html_ad1754d9c2a563f5ad3db72b84e42d03d"><div class="ttname"><a href="struct_bam_tools_1_1_sam_program.html#ad1754d9c2a563f5ad3db72b84e42d03d">BamTools::SamProgram::CommandLine</a></div><div class="ttdeci">std::string CommandLine</div><div class="ttdoc">corresponds to @PG CL:<CommandLine> </div><div class="ttdef"><b>Definition:</b> SamProgram.h:40</div></div>
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