Merge pull request #328 from bioinfo-chru-strasbourg/docs_help

docs Docs #4
bioinfo-chru-strasbourg · Dec 11, 2024 · f6bd475 · f6bd475
2 parents 1aa23f5 + 312953e
commit f6bd475
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diff --git a/README.pdf b/README.pdf
diff --git a/RELEASE_NOTES.html b/RELEASE_NOTES.html
@@ -228,6 +228,8 @@ <h3 data-number="1.1.3" id="fixes"><span
 <li>Fix packages releases</li>
 <li>Fix parameters and configuration files options</li>
 <li>Fix calculations list and parametrization</li>
+<li>Fix empty file export</li>
+<li>Fix BED annotation with parquet method</li>
 <li>More explicite log messages</li>
 </ul>
 <h2 data-number="1.2" id="section-1"><span

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -44,6 +44,8 @@ operations, confugation files in YAML format, and python packages stability.
 - Fix packages releases
 - Fix parameters and configuration files options
 - Fix calculations list and parametrization
+- Fix empty file export
+- Fix BED annotation with parquet method
 - More explicite log messages
 
 ## 0.11.0

diff --git a/RELEASE_NOTES.pdf b/RELEASE_NOTES.pdf
diff --git a/docs/docs.pdf b/docs/docs.pdf
diff --git a/docs/help.configuration.calculation.pdf b/docs/help.configuration.calculation.pdf
diff --git a/docs/help.configuration.pdf b/docs/help.configuration.pdf
diff --git a/docs/help.configuration.prioritization.pdf b/docs/help.configuration.prioritization.pdf
diff --git a/docs/help.parameters.databases.pdf b/docs/help.parameters.databases.pdf
diff --git a/docs/help.parameters.pdf b/docs/help.parameters.pdf
diff --git a/docs/help.pdf b/docs/help.pdf
diff --git a/docs/pdoc/howard/objects/database.html b/docs/pdoc/howard/objects/database.html
diff --git a/docs/pdoc/howard/objects/variants.html b/docs/pdoc/howard/objects/variants.html
@@ -6629,7 +6629,7 @@ <h1 class="modulename">
 </span><span id="L-6234"><a href="#L-6234"><span class="linenos"> 6234</span></a><span class="s2">                                &quot;&quot;&quot;</span>
 </span><span id="L-6235"><a href="#L-6235"><span class="linenos"> 6235</span></a>                                <span class="p">)</span>
 </span><span id="L-6236"><a href="#L-6236"><span class="linenos"> 6236</span></a>                                <span class="n">sql_query_annotation_to_agregate</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-</span><span id="L-6237"><a href="#L-6237"><span class="linenos"> 6237</span></a>                                    <span class="sa">f</span><span class="s2">&quot;&quot;&quot; string_agg(DISTINCT table_parquet_from.&quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot;, &#39;,&#39;) AS &quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot; &quot;&quot;&quot;</span>
+</span><span id="L-6237"><a href="#L-6237"><span class="linenos"> 6237</span></a>                                    <span class="sa">f</span><span class="s2">&quot;&quot;&quot; string_agg(table_parquet_from.&quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot;, &#39;,&#39;) AS &quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot; &quot;&quot;&quot;</span>
 </span><span id="L-6238"><a href="#L-6238"><span class="linenos"> 6238</span></a>                                <span class="p">)</span>
 </span><span id="L-6239"><a href="#L-6239"><span class="linenos"> 6239</span></a>
 </span><span id="L-6240"><a href="#L-6240"><span class="linenos"> 6240</span></a>                        <span class="c1"># Not to annotate</span>
@@ -18422,7 +18422,7 @@ <h1 class="modulename">
 </span><span id="Variants-6235"><a href="#Variants-6235"><span class="linenos"> 6235</span></a><span class="s2">                                &quot;&quot;&quot;</span>
 </span><span id="Variants-6236"><a href="#Variants-6236"><span class="linenos"> 6236</span></a>                                <span class="p">)</span>
 </span><span id="Variants-6237"><a href="#Variants-6237"><span class="linenos"> 6237</span></a>                                <span class="n">sql_query_annotation_to_agregate</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-</span><span id="Variants-6238"><a href="#Variants-6238"><span class="linenos"> 6238</span></a>                                    <span class="sa">f</span><span class="s2">&quot;&quot;&quot; string_agg(DISTINCT table_parquet_from.&quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot;, &#39;,&#39;) AS &quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot; &quot;&quot;&quot;</span>
+</span><span id="Variants-6238"><a href="#Variants-6238"><span class="linenos"> 6238</span></a>                                    <span class="sa">f</span><span class="s2">&quot;&quot;&quot; string_agg(table_parquet_from.&quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot;, &#39;,&#39;) AS &quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot; &quot;&quot;&quot;</span>
 </span><span id="Variants-6239"><a href="#Variants-6239"><span class="linenos"> 6239</span></a>                                <span class="p">)</span>
 </span><span id="Variants-6240"><a href="#Variants-6240"><span class="linenos"> 6240</span></a>
 </span><span id="Variants-6241"><a href="#Variants-6241"><span class="linenos"> 6241</span></a>                        <span class="c1"># Not to annotate</span>
@@ -32655,7 +32655,7 @@ <h6 id="returns">Returns</h6>
 </span><span id="Variants.annotation_parquet-6235"><a href="#Variants.annotation_parquet-6235"><span class="linenos">6235</span></a><span class="s2">                                &quot;&quot;&quot;</span>
 </span><span id="Variants.annotation_parquet-6236"><a href="#Variants.annotation_parquet-6236"><span class="linenos">6236</span></a>                                <span class="p">)</span>
 </span><span id="Variants.annotation_parquet-6237"><a href="#Variants.annotation_parquet-6237"><span class="linenos">6237</span></a>                                <span class="n">sql_query_annotation_to_agregate</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-</span><span id="Variants.annotation_parquet-6238"><a href="#Variants.annotation_parquet-6238"><span class="linenos">6238</span></a>                                    <span class="sa">f</span><span class="s2">&quot;&quot;&quot; string_agg(DISTINCT table_parquet_from.&quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot;, &#39;,&#39;) AS &quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot; &quot;&quot;&quot;</span>
+</span><span id="Variants.annotation_parquet-6238"><a href="#Variants.annotation_parquet-6238"><span class="linenos">6238</span></a>                                    <span class="sa">f</span><span class="s2">&quot;&quot;&quot; string_agg(table_parquet_from.&quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot;, &#39;,&#39;) AS &quot;</span><span class="si">{</span><span class="n">annotation_field_column</span><span class="si">}</span><span class="s2">&quot; &quot;&quot;&quot;</span>
 </span><span id="Variants.annotation_parquet-6239"><a href="#Variants.annotation_parquet-6239"><span class="linenos">6239</span></a>                                <span class="p">)</span>
 </span><span id="Variants.annotation_parquet-6240"><a href="#Variants.annotation_parquet-6240"><span class="linenos">6240</span></a>
 </span><span id="Variants.annotation_parquet-6241"><a href="#Variants.annotation_parquet-6241"><span class="linenos">6241</span></a>                        <span class="c1"># Not to annotate</span>

diff --git a/docs/tips.pdf b/docs/tips.pdf
diff --git a/docs/user_guide.pdf b/docs/user_guide.pdf
diff --git a/plugins/README.pdf b/plugins/README.pdf