Merge pull request #186 from clara-genomics/jdaw/update-html-doc

[docs] update cudamapper html docs

cudamapper/CMakeLists.txt

@@ -45,7 +45,7 @@ target_include_directories(overlapper_triggerred PUBLIC include)
 target_link_libraries(overlapper_triggerred logging utils cgaio)
 target_compile_options(overlapper_triggerred PRIVATE -Werror)
 
-add_doxygen_source_dir(${CMAKE_CURRENT_SOURCE_DIR}/include/cudamapper)
+add_doxygen_source_dir(${CMAKE_CURRENT_SOURCE_DIR}/include)
 
 cuda_add_executable(cudamapper
         src/cudamapper.cpp

cudamapper/include/claragenomics/cudamapper/overlapper.hpp

@@ -20,7 +20,9 @@ namespace cudamapper
 {
 /// \addtogroup cudamapper
 /// \{
-/// Overlapper - given anchors and a read index, calculates overlaps between reads
+
+/// class Overlapper
+/// Given anchors and a read index, calculates overlaps between reads
 class Overlapper
 {
 public:

docs/cpp/aligner_8hpp_source.html

@@ -22,7 +22,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">ClaraGenomicsAnalysis
-   &#160;<span id="projectnumber">0.2.0</span>
+   &#160;<span id="projectnumber">0.3.0</span>
    </div>
   </td>
  </tr>
@@ -107,30 +107,27 @@
 <div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160; </div>
 <div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">sync_alignments</a>() = 0;</div>
 <div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160; </div>
-<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">add_alignment</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* query, int32_t query_length, <span class="keyword">const</span> <span class="keywordtype">char</span>* target, int32_t target_length) = 0;</div>
-<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160; </div>
-<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;std::shared_ptr&lt;Alignment&gt;&gt;&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">get_alignments</a>() <span class="keyword">const</span> = 0;</div>
-<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160; </div>
-<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a35db72e196fdc4b0bc165ad8e7548af3">set_cuda_stream</a>(cudaStream_t stream) = 0;</div>
+<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">add_alignment</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* query, int32_t query_length, <span class="keyword">const</span> <span class="keywordtype">char</span>* target, int32_t target_length) = 0;</div>
+<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160; </div>
+<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;std::shared_ptr&lt;Alignment&gt;&gt;&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">get_alignments</a>() <span class="keyword">const</span> = 0;</div>
+<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160; </div>
+<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">reset</a>() = 0;</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; </div>
-<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">reset</a>() = 0;</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; </div>
-<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;std::unique_ptr&lt;Aligner&gt; <a class="code" href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">create_aligner</a>(int32_t max_query_length, int32_t max_target_length, int32_t max_alignments, <a class="code" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> type, cudaStream_t stream, int32_t device_id);</div>
-<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160; </div>
-<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;} <span class="comment">// namespace cudaaligner</span></div>
-<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
+<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;std::unique_ptr&lt;Aligner&gt; <a class="code" href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">create_aligner</a>(int32_t max_query_length, int32_t max_target_length, int32_t max_alignments, <a class="code" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> type, cudaStream_t stream, int32_t device_id);</div>
+<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160; </div>
+<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;} <span class="comment">// namespace cudaaligner</span></div>
+<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
 </div><!-- fragment --></div><!-- contents -->
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">claragenomics::cudaaligner::Aligner</a></div><div class="ttdef"><b>Definition:</b> aligner.hpp:33</div></div>
 <div class="ttc" id="agroup__cudaaligner_html_ga07b5416cfe8a05f326cb244f9d596449"><div class="ttname"><a href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">claragenomics::cudaaligner::create_aligner</a></div><div class="ttdeci">std::unique_ptr&lt; Aligner &gt; create_aligner(int32_t max_query_length, int32_t max_target_length, int32_t max_alignments, AlignmentType type, cudaStream_t stream, int32_t device_id)</div><div class="ttdoc">Created Aligner object.</div></div>
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_aaae329eae2ed3e364db643163755e987"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">claragenomics::cudaaligner::Aligner::~Aligner</a></div><div class="ttdeci">virtual ~Aligner()=default</div><div class="ttdoc">Virtual destructor for Aligner.</div></div>
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a8b3c20782b9eaa4c2219fb7ff51772db"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">claragenomics::cudaaligner::Aligner::align_all</a></div><div class="ttdeci">virtual StatusType align_all()=0</div><div class="ttdoc">Launch CUDA accelerated alignment.</div></div>
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a1d775f9821ce3ecdcdc67cb07f35a4d8"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">claragenomics::cudaaligner::Aligner::get_alignments</a></div><div class="ttdeci">virtual const std::vector&lt; std::shared_ptr&lt; Alignment &gt; &gt; &amp; get_alignments() const =0</div><div class="ttdoc">Return the computed alignments.</div></div>
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_ac929b7ba836dfac74d8975f652563482"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">claragenomics::cudaaligner::Aligner::sync_alignments</a></div><div class="ttdeci">virtual StatusType sync_alignments()=0</div><div class="ttdoc">Waits for CUDA accelerated alignment to finish.</div></div>
-<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a35db72e196fdc4b0bc165ad8e7548af3"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a35db72e196fdc4b0bc165ad8e7548af3">claragenomics::cudaaligner::Aligner::set_cuda_stream</a></div><div class="ttdeci">virtual void set_cuda_stream(cudaStream_t stream)=0</div><div class="ttdoc">Set CUDA stream for aligner.</div></div>
 <div class="ttc" id="agroup__cudaaligner_html_gafcccbe51c86f9772ccf837fc433f518b"><div class="ttname"><a href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">claragenomics::cudaaligner::AlignmentType</a></div><div class="ttdeci">AlignmentType</div><div class="ttdoc">AlignmentType - Enum for storing type of alignment.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:36</div></div>
 <div class="ttc" id="agroup__cudaaligner_html_ga7d6424e11f69650b1d4eabef0cf4f602"><div class="ttname"><a href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">claragenomics::cudaaligner::StatusType</a></div><div class="ttdeci">StatusType</div><div class="ttdoc">CUDA Aligner error type.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:25</div></div>
-<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_adc32085da2b5681f0045d05c43a35f92"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">claragenomics::cudaaligner::Aligner::add_alignment</a></div><div class="ttdeci">virtual StatusType add_alignment(const char *query, int32_t query_length, const char *target, int32_t target_length)=0</div><div class="ttdoc">Add new alignment object.</div></div>
+<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_adc32085da2b5681f0045d05c43a35f92"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">claragenomics::cudaaligner::Aligner::add_alignment</a></div><div class="ttdeci">virtual StatusType add_alignment(const char *query, int32_t query_length, const char *target, int32_t target_length)=0</div><div class="ttdoc">Add new alignment object. Only strings with characters from the alphabet [ACGT] are guaranteed to pro...</div></div>
 <div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a9f7f056a269c32c909a9bfb7132ba439"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">claragenomics::cudaaligner::Aligner::reset</a></div><div class="ttdeci">virtual void reset()=0</div><div class="ttdoc">Reset aligner object.</div></div>
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>

docs/cpp/alignment_8hpp_source.html

@@ -22,7 +22,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">ClaraGenomicsAnalysis
-   &#160;<span id="projectnumber">0.2.0</span>
+   &#160;<span id="projectnumber">0.3.0</span>
    </div>
   </td>
  </tr>
@@ -94,7 +94,7 @@
 <div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="keyword">namespace </span>cudaaligner</div>
 <div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;{</div>
 <div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160; </div>
-<div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">   31</a></span>&#160;<span class="keyword">using</span> <a class="code" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a> = std::pair&lt;std::string, std::string&gt;;</div>
+<div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">   31</a></span>&#160;<span class="keyword">typedef</span> std::pair&lt;std::string, std::string&gt; <a class="code" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a>;</div>
 <div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
 <div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">   34</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a></div>
 <div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;{</div>