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LTLA committed Feb 5, 2025
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125 changes: 63 additions & 62 deletions docs/atomic__vector_8hpp_source.html
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71 changes: 36 additions & 35 deletions docs/bam__file_8hpp_source.html
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Original file line number Diff line number Diff line change
Expand Up @@ -110,42 +110,43 @@
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> </div>
<div class="foldopen" id="foldopen00033" data-start="{" data-end="}">
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"><a class="line" href="namespacetakane_1_1bam__file.html#adabb2d53e3bcafb8771d453ea76bd80a"> 33</a></span><span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code hl_function" href="namespacetakane_1_1bam__file.html#adabb2d53e3bcafb8771d453ea76bd80a">validate</a>(<span class="keyword">const</span> std::filesystem::path&amp; path, <span class="keyword">const</span> <a class="code hl_struct" href="structtakane_1_1ObjectMetadata.html">ObjectMetadata</a>&amp; metadata, <a class="code hl_struct" href="structtakane_1_1Options.html">Options</a>&amp; options) {</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">const</span> std::string&amp; vstring = internal_json::extract_version_for_type(metadata.<a class="code hl_variable" href="structtakane_1_1ObjectMetadata.html#a3b46efa17e6ca667bc902073cf7151cd">other</a>, <span class="stringliteral">&quot;bam_file&quot;</span>);</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">auto</span> version = ritsuko::parse_version_string(vstring.c_str(), vstring.size(), <span class="comment">/* skip_patch = */</span> <span class="keyword">true</span>);</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keywordflow">if</span> (version.major != 1) {</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">&quot;unsupported version string &#39;&quot;</span> + vstring + <span class="stringliteral">&quot;&#39;&quot;</span>);</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> }</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="comment">// Magic numbers taken from https://samtools.github.io/hts-specs/SAMv1.pdf</span></div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">auto</span> ipath = path / <span class="stringliteral">&quot;file.bam&quot;</span>;</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> internal_files::check_gzip_signature(ipath);</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> internal_files::check_signature&lt;byteme::GzipFileReader&gt;(ipath, <span class="stringliteral">&quot;BAM\1&quot;</span>, 4, <span class="stringliteral">&quot;BAM&quot;</span>);</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">auto</span> ixpath = ipath;</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> ixpath += <span class="stringliteral">&quot;.bai&quot;</span>;</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">if</span> (std::filesystem::exists(ixpath)) {</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> internal_files::check_signature(ixpath, <span class="stringliteral">&quot;BAI\1&quot;</span>, 4, <span class="stringliteral">&quot;BAM index&quot;</span>);</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> }</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> <span class="comment">// Magic number taken from https://samtools.github.io/hts-specs/CSIv1.pdf</span></div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> ixpath = ipath;</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> ixpath += <span class="stringliteral">&quot;.csi&quot;</span>;</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="keywordflow">if</span> (std::filesystem::exists(ixpath)) {</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> internal_files::check_gzip_signature(ixpath);</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> internal_files::check_signature&lt;byteme::GzipFileReader&gt;(ixpath, <span class="stringliteral">&quot;CSI\1&quot;</span>, 4, <span class="stringliteral">&quot;CSI index&quot;</span>);</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> }</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="keywordflow">if</span> (options.<a class="code hl_variable" href="structtakane_1_1Options.html#a572c7071276f7318276354eb658a93cb">bam_file_strict_check</a>) {</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> options.<a class="code hl_variable" href="structtakane_1_1Options.html#a572c7071276f7318276354eb658a93cb">bam_file_strict_check</a>(path, metadata, options);</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> }</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span>}</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">const</span> std::string type_name = <span class="stringliteral">&quot;bam_file&quot;</span>; <span class="comment">// use a separate variable to avoid dangling reference warnings from GCC.</span></div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">const</span> std::string&amp; vstring = internal_json::extract_version_for_type(metadata.<a class="code hl_variable" href="structtakane_1_1ObjectMetadata.html#a3b46efa17e6ca667bc902073cf7151cd">other</a>, type_name);</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">auto</span> version = ritsuko::parse_version_string(vstring.c_str(), vstring.size(), <span class="comment">/* skip_patch = */</span> <span class="keyword">true</span>);</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> <span class="keywordflow">if</span> (version.major != 1) {</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">&quot;unsupported version string &#39;&quot;</span> + vstring + <span class="stringliteral">&quot;&#39;&quot;</span>);</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> }</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> </div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="comment">// Magic numbers taken from https://samtools.github.io/hts-specs/SAMv1.pdf</span></div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keyword">auto</span> ipath = path / <span class="stringliteral">&quot;file.bam&quot;</span>;</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> internal_files::check_gzip_signature(ipath);</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> internal_files::check_signature&lt;byteme::GzipFileReader&gt;(ipath, <span class="stringliteral">&quot;BAM\1&quot;</span>, 4, <span class="stringliteral">&quot;BAM&quot;</span>);</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">auto</span> ixpath = ipath;</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> ixpath += <span class="stringliteral">&quot;.bai&quot;</span>;</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="keywordflow">if</span> (std::filesystem::exists(ixpath)) {</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> internal_files::check_signature(ixpath, <span class="stringliteral">&quot;BAI\1&quot;</span>, 4, <span class="stringliteral">&quot;BAM index&quot;</span>);</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> }</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="comment">// Magic number taken from https://samtools.github.io/hts-specs/CSIv1.pdf</span></div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> ixpath = ipath;</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> ixpath += <span class="stringliteral">&quot;.csi&quot;</span>;</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <span class="keywordflow">if</span> (std::filesystem::exists(ixpath)) {</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> internal_files::check_gzip_signature(ixpath);</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> internal_files::check_signature&lt;byteme::GzipFileReader&gt;(ixpath, <span class="stringliteral">&quot;CSI\1&quot;</span>, 4, <span class="stringliteral">&quot;CSI index&quot;</span>);</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> }</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> </div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <span class="keywordflow">if</span> (options.<a class="code hl_variable" href="structtakane_1_1Options.html#a572c7071276f7318276354eb658a93cb">bam_file_strict_check</a>) {</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> options.<a class="code hl_variable" href="structtakane_1_1Options.html#a572c7071276f7318276354eb658a93cb">bam_file_strict_check</a>(path, metadata, options);</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> }</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span>}</div>
</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span>}</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span>}</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span><span class="preprocessor">#endif</span></div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span>}</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span>}</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="anamespacetakane_1_1bam__file_html_adabb2d53e3bcafb8771d453ea76bd80a"><div class="ttname"><a href="namespacetakane_1_1bam__file.html#adabb2d53e3bcafb8771d453ea76bd80a">takane::bam_file::validate</a></div><div class="ttdeci">void validate(const std::filesystem::path &amp;path, const ObjectMetadata &amp;metadata, Options &amp;options)</div><div class="ttdef"><b>Definition</b> bam_file.hpp:33</div></div>
<div class="ttc" id="anamespacetakane_html"><div class="ttname"><a href="namespacetakane.html">takane</a></div><div class="ttdoc">takane validation functions.</div><div class="ttdef"><b>Definition</b> _derived_from.hpp:15</div></div>
<div class="ttc" id="astructtakane_1_1ObjectMetadata_html"><div class="ttname"><a href="structtakane_1_1ObjectMetadata.html">takane::ObjectMetadata</a></div><div class="ttdoc">Object metadata, including the type and other fields.</div><div class="ttdef"><b>Definition</b> utils_public.hpp:26</div></div>
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