build based on 96f4eb9

dev/index.html

@@ -3,4 +3,4 @@
 pkg"add https://github.com/OpenMendel/SnpArrays.jl"
 pkg"add https://github.com/OpenMendel/VCFTools.jl"
 pkg"add https://github.com/OpenMendel/BGEN.jl"
-pkg&quot;add https://github.com/OpenMendel/MendelImpute.jl&quot;</code></pre><p>This package supports Julia <code>v1.6</code>+.</p><h2 id="Manual-Outline"><a class="docs-heading-anchor" href="#Manual-Outline">Manual Outline</a><a id="Manual-Outline-1"></a><a class="docs-heading-anchor-permalink" href="#Manual-Outline" title="Permalink"></a></h2><ul><li><a href="man/Phasing_and_Imputation/#Preparing-Target-Data">Preparing Target Data</a></li><li><a href="man/Phasing_and_Imputation/#Preparing-Reference-Haplotype-Panel">Preparing Reference Haplotype Panel</a></li><li><a href="man/Phasing_and_Imputation/#Detailed-Example">Detailed Example</a></li><li class="no-marker"><ul><li><a href="man/Phasing_and_Imputation/#Step-1:-generating-realistic-reference-and-target-data">Step 1: generating realistic reference and target data</a></li><li><a href="man/Phasing_and_Imputation/#Step-2:-generating-.jlso-compressed-reference-panel">Step 2: generating <code>.jlso</code> compressed reference panel</a></li><li><a href="man/Phasing_and_Imputation/#Step-3:-Run-imputation-and-phasing">Step 3: Run imputation and phasing</a></li><li><a href="man/Phasing_and_Imputation/#Step-3.5:-(only-for-simulated-data)-check-imputation-accuracy">Step 3.5: (only for simulated data) check imputation accuracy</a></li><li><a href="man/Phasing_and_Imputation/#Post-imputation:-per-SNP-Imputation-Quality-Score">Post-imputation: per-SNP Imputation Quality Score</a></li><li><a href="man/Phasing_and_Imputation/#Post-imputation:-per-sample-Imputation-Quality-score">Post-imputation: per-sample Imputation Quality score</a></li></ul></li><li><a href="man/performance/#Performance-gotchas">Performance gotchas</a></li><li class="no-marker"><ul><li><a href="man/performance/#First-time-performance">First time performance</a></li><li><a href="man/performance/#Run-MendelImpute-in-parallel">Run MendelImpute in parallel</a></li><li><a href="man/performance/#Compressing-haplotype-panels-is-slow">Compressing haplotype panels is slow</a></li><li><a href="man/performance/#max_d-too-high-(or-too-low)"><code>max_d</code> too high (or too low)</a></li><li><a href="man/performance/#Do-you-have-enough-memory-(RAM)?">Do you have enough memory (RAM)?</a></li></ul></li><li><a href="man/painting/#Estimating-ancestry">Estimating ancestry</a></li><li class="no-marker"><ul><li><a href="man/painting/#Prepare-Example-data-for-illustration">Prepare Example data for illustration</a></li><li><a href="man/painting/#Global-ancestry-inference">Global ancestry inference</a></li><li><a href="man/painting/#Local-ancestry-inference">Local ancestry inference</a></li></ul></li><li><a href="man/ultra+compress/#Ultra-compressed-format">Ultra-compressed format</a></li><li class="no-marker"><ul><li><a href="man/ultra+compress/#Saving">Saving</a></li><li><a href="man/ultra+compress/#Loading">Loading</a></li></ul></li><li><a href="man/script/#Run-MendelImpute-as-script">Run MendelImpute as script</a></li><li><a href="man/api/#API">API</a></li><li class="no-marker"><ul><li><a href="man/api/#Index">Index</a></li><li><a href="man/api/#Functions">Functions</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/Phasing_and_Imputation/">Phasing and Imputation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 30 July 2023 02:28">Sunday 30 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+pkg&quot;add https://github.com/OpenMendel/MendelImpute.jl&quot;</code></pre><p>This package supports Julia <code>v1.6</code>+.</p><h2 id="Manual-Outline"><a class="docs-heading-anchor" href="#Manual-Outline">Manual Outline</a><a id="Manual-Outline-1"></a><a class="docs-heading-anchor-permalink" href="#Manual-Outline" title="Permalink"></a></h2><ul><li><a href="man/Phasing_and_Imputation/#Preparing-Target-Data">Preparing Target Data</a></li><li><a href="man/Phasing_and_Imputation/#Preparing-Reference-Haplotype-Panel">Preparing Reference Haplotype Panel</a></li><li><a href="man/Phasing_and_Imputation/#Detailed-Example">Detailed Example</a></li><li class="no-marker"><ul><li><a href="man/Phasing_and_Imputation/#Step-1:-generating-realistic-reference-and-target-data">Step 1: generating realistic reference and target data</a></li><li><a href="man/Phasing_and_Imputation/#Step-2:-generating-.jlso-compressed-reference-panel">Step 2: generating <code>.jlso</code> compressed reference panel</a></li><li><a href="man/Phasing_and_Imputation/#Step-3:-Run-imputation-and-phasing">Step 3: Run imputation and phasing</a></li><li><a href="man/Phasing_and_Imputation/#Step-3.5:-(only-for-simulated-data)-check-imputation-accuracy">Step 3.5: (only for simulated data) check imputation accuracy</a></li><li><a href="man/Phasing_and_Imputation/#Post-imputation:-per-SNP-Imputation-Quality-Score">Post-imputation: per-SNP Imputation Quality Score</a></li><li><a href="man/Phasing_and_Imputation/#Post-imputation:-per-sample-Imputation-Quality-score">Post-imputation: per-sample Imputation Quality score</a></li></ul></li><li><a href="man/performance/#Performance-gotchas">Performance gotchas</a></li><li class="no-marker"><ul><li><a href="man/performance/#First-time-performance">First time performance</a></li><li><a href="man/performance/#Run-MendelImpute-in-parallel">Run MendelImpute in parallel</a></li><li><a href="man/performance/#Compressing-haplotype-panels-is-slow">Compressing haplotype panels is slow</a></li><li><a href="man/performance/#max_d-too-high-(or-too-low)"><code>max_d</code> too high (or too low)</a></li><li><a href="man/performance/#Do-you-have-enough-memory-(RAM)?">Do you have enough memory (RAM)?</a></li></ul></li><li><a href="man/painting/#Estimating-ancestry">Estimating ancestry</a></li><li class="no-marker"><ul><li><a href="man/painting/#Prepare-Example-data-for-illustration">Prepare Example data for illustration</a></li><li><a href="man/painting/#Global-ancestry-inference">Global ancestry inference</a></li><li><a href="man/painting/#Local-ancestry-inference">Local ancestry inference</a></li></ul></li><li><a href="man/ultra+compress/#Ultra-compressed-format">Ultra-compressed format</a></li><li class="no-marker"><ul><li><a href="man/ultra+compress/#Saving">Saving</a></li><li><a href="man/ultra+compress/#Loading">Loading</a></li></ul></li><li><a href="man/script/#Run-MendelImpute-as-script">Run MendelImpute as script</a></li><li><a href="man/api/#API">API</a></li><li class="no-marker"><ul><li><a href="man/api/#Index">Index</a></li><li><a href="man/api/#Functions">Functions</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/Phasing_and_Imputation/">Phasing and Imputation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 31 July 2023 02:27">Monday 31 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/Phasing_and_Imputation/index.html

@@ -145,4 +145,4 @@
 
 # visualize error distribution
 histogram(quality[:error], label=:none, xlabel="per-sample quality score",
-    ylabel=&quot;Number of samples&quot;) </code></pre><p><img src="../output_20_0.svg" alt="svg"/></p><p><strong>Conclusion:</strong> Most samples are well imputed (e.g. score close to 1), but some samples are indeed poorly imputed. From the histogram, we can safely <a href="https://openmendel.github.io/VCFTools.jl/dev/man/filter/#Subsetting-VCF-files-using-array-masks">filtered out</a> samples with score <span>$&lt; 0.999$</span> as that would remove poorly imputed individuals without reducing sample size too much.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../performance/">Performance Gotchas »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 30 July 2023 02:28">Sunday 30 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    ylabel=&quot;Number of samples&quot;) </code></pre><p><img src="../output_20_0.svg" alt="svg"/></p><p><strong>Conclusion:</strong> Most samples are well imputed (e.g. score close to 1), but some samples are indeed poorly imputed. From the histogram, we can safely <a href="https://openmendel.github.io/VCFTools.jl/dev/man/filter/#Subsetting-VCF-files-using-array-masks">filtered out</a> samples with score <span>$&lt; 0.999$</span> as that would remove poorly imputed individuals without reducing sample size too much.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../performance/">Performance Gotchas »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 31 July 2023 02:27">Monday 31 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>