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monarch-initiative · Dec 4, 2024 · eac471f · eac471f
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diff --git a/api/pheval/prepare/prepare_corpus/index.html b/api/pheval/prepare/prepare_corpus/index.html
@@ -1536,7 +1536,12 @@ <h2 id="src.pheval.prepare.prepare_corpus.prepare_corpus" class="doc doc-heading
 <span class="normal">87</span>
 <span class="normal">88</span>
 <span class="normal">89</span>
-<span class="normal">90</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">prepare_corpus</span><span class="p">(</span>
+<span class="normal">90</span>
+<span class="normal">91</span>
+<span class="normal">92</span>
+<span class="normal">93</span>
+<span class="normal">94</span>
+<span class="normal">95</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">prepare_corpus</span><span class="p">(</span>
     <span class="n">phenopacket_dir</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
     <span class="n">variant_analysis</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
     <span class="n">gene_analysis</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
@@ -1583,6 +1588,11 @@ <h2 id="src.pheval.prepare.prepare_corpus.prepare_corpus" class="doc doc-heading
                     <span class="sa">f</span><span class="s2">&quot;Removed </span><span class="si">{</span><span class="n">phenopacket_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> from the corpus due to missing variant fields.&quot;</span>
                 <span class="p">)</span>
                 <span class="k">continue</span>
+            <span class="k">elif</span> <span class="n">phenopacket_util</span><span class="o">.</span><span class="n">check_variant_alleles</span><span class="p">():</span>
+                <span class="n">info_log</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+                    <span class="sa">f</span><span class="s2">&quot;Removed </span><span class="si">{</span><span class="n">phenopacket_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> from the corpus due to identical &quot;</span>
+                    <span class="s2">&quot;reference and alternate allele fields.&quot;</span>
+                <span class="p">)</span>
         <span class="k">if</span> <span class="n">gene_analysis</span><span class="p">:</span>
             <span class="k">if</span> <span class="n">phenopacket_util</span><span class="o">.</span><span class="n">check_incomplete_gene_record</span><span class="p">():</span>
                 <span class="n">info_log</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>

diff --git a/api/pheval/utils/phenopacket_utils/index.html b/api/pheval/utils/phenopacket_utils/index.html
diff --git a/developing_a_pheval_plugin/index.html b/developing_a_pheval_plugin/index.html
@@ -2265,7 +2265,20 @@ <h4 id="utility-methods">Utility methods</h4>
 <span class="normal">531</span>
 <span class="normal">532</span>
 <span class="normal">533</span>
-<span class="normal">534</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">PhenopacketUtil</span><span class="p">:</span>
+<span class="normal">534</span>
+<span class="normal">535</span>
+<span class="normal">536</span>
+<span class="normal">537</span>
+<span class="normal">538</span>
+<span class="normal">539</span>
+<span class="normal">540</span>
+<span class="normal">541</span>
+<span class="normal">542</span>
+<span class="normal">543</span>
+<span class="normal">544</span>
+<span class="normal">545</span>
+<span class="normal">546</span>
+<span class="normal">547</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">PhenopacketUtil</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Class for retrieving data from a Phenopacket or Family object&quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">phenopacket_contents</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Phenopacket</span><span class="p">,</span> <span class="n">Family</span><span class="p">]):</span>
@@ -2552,6 +2565,19 @@ <h4 id="utility-methods">Utility methods</h4>
                 <span class="k">return</span> <span class="kc">True</span>
         <span class="k">return</span> <span class="kc">False</span>
 
+    <span class="k">def</span> <span class="nf">check_variant_alleles</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Check if any variant record in the phenopacket has identical reference and alternate alleles.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            bool: True if the reference and alternate alleles are identical, False otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">variants</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">diagnosed_variants</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">variant</span> <span class="ow">in</span> <span class="n">variants</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">variant</span><span class="o">.</span><span class="n">ref</span> <span class="o">==</span> <span class="n">variant</span><span class="o">.</span><span class="n">alt</span><span class="p">:</span>
+                <span class="k">return</span> <span class="kc">True</span>
+        <span class="k">return</span> <span class="kc">False</span>
+
     <span class="k">def</span> <span class="nf">check_incomplete_gene_record</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Check if any gene record in the phenopacket has incomplete information.</span>

diff --git a/objects.inv b/objects.inv
diff --git a/search/search_index.json b/search/search_index.json
diff --git a/sitemap.xml b/sitemap.xml
@@ -2,178 +2,178 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
     <url>
          <loc>https://monarch-initiative.github.io/pheval/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/CODE_OF_CONDUCT/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/about/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/contact/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/contributing/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/developing_a_pheval_plugin/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/executing_a_benchmark/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/exomiser_pipeline/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/pipeline/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/plugins/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/roadmap/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/styleguide/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/cli/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/config_parser/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/run_metadata/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/analysis/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/assess_prioritisation_base/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/benchmark_db_manager/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/benchmark_generator/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/benchmarking_data/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/binary_classification_stats/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/disease_prioritisation_analysis/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/gene_prioritisation_analysis/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/generate_plots/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/generate_summary_outputs/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/parse_benchmark_summary/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/parse_corpus/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/prioritisation_result_types/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/rank_stats/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/run_data_parser/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/variant_prioritisation_analysis/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/infra/exomiserdb/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/post_processing/post_processing/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/create_noisy_phenopackets/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/create_spiked_vcf/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/custom_exceptions/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/prepare_corpus/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/update_phenopacket/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/runners/runner/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/exomiser/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/file_utils/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/phenopacket_utils/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/semsim_utils/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
     <url>
          <loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/utils/</loc>
-         <lastmod>2024-10-23</lastmod>
+         <lastmod>2024-12-04</lastmod>
     </url>
 </urlset>
diff --git a/sitemap.xml.gz b/sitemap.xml.gz