deploy: 7348218

latest/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 7532f1c609e81d01e8824fd5d347b4b4
+config: 69e796f117a679d0e01b7ccc6f2c9d4c
 tags: 645f666f9bcd5a90fca523b33c5a78b7

latest/Af1.html

@@ -864,7 +864,7 @@ <h2>Fst analysis<a class="headerlink" href="#fst-analysis" title="Link to this h
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/Ag3.html

@@ -462,22 +462,25 @@ <h2>Sample metadata access<a class="headerlink" href="#sample-metadata-access" t
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.clear_extra_metadata.html#malariagen_data.ag3.Ag3.clear_extra_metadata" title="malariagen_data.ag3.Ag3.clear_extra_metadata"><code class="xref py py-obj docutils literal notranslate"><span class="pre">clear_extra_metadata</span></code></a>()</p></td>
 <td><p>Clear any extra metadata previously added.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.count_samples.html#malariagen_data.ag3.Ag3.count_samples" title="malariagen_data.ag3.Ag3.count_samples"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_samples</span></code></a>([sample_sets, sample_query, ...])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.cross_metadata.html#malariagen_data.ag3.Ag3.cross_metadata" title="malariagen_data.ag3.Ag3.cross_metadata"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cross_metadata</span></code></a>()</p></td>
+<td><p>Load a dataframe containing metadata about samples in colony crosses, including which samples are parents or progeny in which crosses.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.count_samples.html#malariagen_data.ag3.Ag3.count_samples" title="malariagen_data.ag3.Ag3.count_samples"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_samples</span></code></a>([sample_sets, sample_query, ...])</p></td>
 <td><p>Create a pivot table showing numbers of samples available by space, time and taxon.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.lookup_sample.html#malariagen_data.ag3.Ag3.lookup_sample" title="malariagen_data.ag3.Ag3.lookup_sample"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lookup_sample</span></code></a>(sample[, sample_set])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.lookup_sample.html#malariagen_data.ag3.Ag3.lookup_sample" title="malariagen_data.ag3.Ag3.lookup_sample"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lookup_sample</span></code></a>(sample[, sample_set])</p></td>
 <td><p>Get the metadata for a specific sample and sample set.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.plot_samples_bar.html#malariagen_data.ag3.Ag3.plot_samples_bar" title="malariagen_data.ag3.Ag3.plot_samples_bar"><code class="xref py py-obj docutils literal notranslate"><span class="pre">plot_samples_bar</span></code></a>(x[, color, sort, ...])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.plot_samples_bar.html#malariagen_data.ag3.Ag3.plot_samples_bar" title="malariagen_data.ag3.Ag3.plot_samples_bar"><code class="xref py py-obj docutils literal notranslate"><span class="pre">plot_samples_bar</span></code></a>(x[, color, sort, ...])</p></td>
 <td><p>Plot a bar chart showing the number of samples available, grouped by some variable such as country or year.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.plot_samples_interactive_map.html#malariagen_data.ag3.Ag3.plot_samples_interactive_map" title="malariagen_data.ag3.Ag3.plot_samples_interactive_map"><code class="xref py py-obj docutils literal notranslate"><span class="pre">plot_samples_interactive_map</span></code></a>([sample_sets, ...])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.plot_samples_interactive_map.html#malariagen_data.ag3.Ag3.plot_samples_interactive_map" title="malariagen_data.ag3.Ag3.plot_samples_interactive_map"><code class="xref py py-obj docutils literal notranslate"><span class="pre">plot_samples_interactive_map</span></code></a>([sample_sets, ...])</p></td>
 <td><p>Plot an interactive map showing sampling locations using ipyleaflet.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.wgs_data_catalog.html#malariagen_data.ag3.Ag3.wgs_data_catalog" title="malariagen_data.ag3.Ag3.wgs_data_catalog"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wgs_data_catalog</span></code></a>(sample_set)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.wgs_data_catalog.html#malariagen_data.ag3.Ag3.wgs_data_catalog" title="malariagen_data.ag3.Ag3.wgs_data_catalog"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wgs_data_catalog</span></code></a>(sample_set)</p></td>
 <td><p>Load a data catalog providing URLs for downloading BAM, VCF and Zarr files for samples in a given sample set.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.cohorts.html#malariagen_data.ag3.Ag3.cohorts" title="malariagen_data.ag3.Ag3.cohorts"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cohorts</span></code></a>(cohort_set)</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.cohorts.html#malariagen_data.ag3.Ag3.cohorts" title="malariagen_data.ag3.Ag3.cohorts"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cohorts</span></code></a>(cohort_set)</p></td>
 <td><p>Read data for a specific cohort set, including cohort size, country code, taxon, administrative units name, ISO code, geoBoundaries shape ID and representative latitude and longitude points.</p></td>
 </tr>
 </tbody>
@@ -887,7 +890,7 @@ <h2>Fst analysis<a class="headerlink" href="#fst-analysis" title="Link to this h
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/Amin1.html

@@ -515,7 +515,7 @@ <h2>SNP data access<a class="headerlink" href="#snp-data-access" title="Link to
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/_sources/Ag3.rst.txt

@@ -49,6 +49,7 @@ Sample metadata access
     sample_metadata
     add_extra_metadata
     clear_extra_metadata
+    cross_metadata
     count_samples
     lookup_sample
     plot_samples_bar

latest/_sources/generated/malariagen_data.ag3.Ag3.cross_metadata.rst.txt

@@ -0,0 +1,6 @@
+malariagen\_data.ag3.Ag3.cross\_metadata
+========================================
+
+.. currentmodule:: malariagen_data.ag3
+
+.. automethod:: Ag3.cross_metadata

latest/generated/malariagen_data.af1.Af1.aa_allele_frequencies.html

@@ -532,7 +532,7 @@ <h2>Notes<a class="headerlink" href="#notes" title="Link to this heading">#</a><
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.aa_allele_frequencies_advanced.html

@@ -542,7 +542,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.add_extra_metadata.html

@@ -487,7 +487,7 @@ <h2>Notes<a class="headerlink" href="#notes" title="Link to this heading">#</a><
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.average_fst.html

@@ -526,7 +526,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.biallelic_diplotype_pairwise_distances.html

@@ -560,7 +560,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.biallelic_diplotypes.html

@@ -561,7 +561,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.biallelic_snp_calls.html

@@ -559,7 +559,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.clear_extra_metadata.html

@@ -472,7 +472,7 @@ <h1>malariagen_data.af1.Af1.clear_extra_metadata<a class="headerlink" href="#mal
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.cnv_coverage_calls.html

@@ -509,7 +509,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.cnv_hmm.html

@@ -516,7 +516,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.cohort_diversity_stats.html

@@ -544,7 +544,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.cohorts.html

@@ -490,7 +490,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.contigs.html

@@ -472,7 +472,7 @@ <h1>malariagen_data.af1.Af1.contigs<a class="headerlink" href="#malariagen-data-
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.count_samples.html

@@ -499,7 +499,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.coverage_calls_analysis_ids.html

@@ -474,7 +474,7 @@ <h1>malariagen_data.af1.Af1.coverage_calls_analysis_ids<a class="headerlink" hre
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.diversity_stats.html

@@ -545,7 +545,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.fst_gwss.html

@@ -534,7 +534,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.g123_calibration.html

@@ -533,7 +533,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.g123_gwss.html

@@ -534,7 +534,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.gene_cnv.html

@@ -502,7 +502,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.gene_cnv_frequencies.html

@@ -515,7 +515,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.gene_cnv_frequencies_advanced.html

@@ -526,7 +526,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.genome_features.html

@@ -492,7 +492,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.genome_sequence.html

@@ -504,7 +504,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.h12_calibration.html

@@ -531,7 +531,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.h12_gwss.html

@@ -532,7 +532,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.h1x_gwss.html

@@ -532,7 +532,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.haplotype_pairwise_distances.html

@@ -527,7 +527,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.haplotype_sites.html

@@ -510,7 +510,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.haplotypes.html

@@ -529,7 +529,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.igv.html

@@ -492,7 +492,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.ihs_gwss.html

@@ -559,7 +559,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.is_accessible.html

@@ -506,7 +506,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.lookup_release.html

@@ -483,7 +483,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>

latest/generated/malariagen_data.af1.Af1.lookup_sample.html

@@ -485,7 +485,7 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">#<
 
   <p class="copyright">
 
-      © Copyright 2023, MalariaGEN.
+      © Copyright 2024, MalariaGEN.
       <br/>
 
   </p>