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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinculo">Debian Med / trinculo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trinculo/-/commit/2a1004df973a13c8a141b0e218e38e00dad9bbd9">2a1004df</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-04-07T21:06:28+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add to maintainers
</pre>
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<strong><a href="https://salsa.debian.org/med-team/trinculo/-/commit/226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae">226a5ea8</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-04-07T21:06:41+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/trinculo/-/compare/51ae677bda3da7b75bded509c58e3642a595b714...226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ Source: trinculo</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org><span class="idiff left right">, Pranav Ballaney <ballaneypranav@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> liblapack-dev</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/trinculo/-/compare/51ae677bda3da7b75bded509c58e3642a595b714...226a5ea833ac0db3323dfc13ba0cc4ca3efa6fae#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,11 +5,11 @@ pkg=trinculo</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left right"> </span></span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="idiff left right"> </span><span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="idiff left right"> </span><span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="idiff left right"> </span><span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"> <span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,31 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--help</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"1. Testing frequentist association (plink)..."</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"2. Testing frequentist association (dosage)..."</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--dosage</span> genotypes.dose <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"3. Testing frequentist association (covariates)..."</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control <span class="nt" style="color: #000080;">--covar</span> pcs.txt </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"4. Testing frequentist association (conditioning)..."</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"SNP1"</span> <span class="o" style="font-weight: 600;">></span> condfile[1]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control <span class="nt" style="color: #000080;">--covar</span> pcs.txt <span class="nt" style="color: #000080;">--condition</span> condfile[1] </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"5. Testing Bayesian association..."</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control <span class="nt" style="color: #000080;">--covar</span> pcs.txt <span class="nt" style="color: #000080;">--normalize</span> <span class="nt" style="color: #000080;">--defaultprior</span> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"6. Testing Bayesian association (prior file)..."</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control <span class="nt" style="color: #000080;">--covar</span> pcs.txt <span class="nt" style="color: #000080;">--normalize</span> <span class="nt" style="color: #000080;">--priors</span> priors.txt </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"7. Testing Bayesian model selection..."</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control <span class="nt" style="color: #000080;">--covar</span> pcs.txt <span class="nt" style="color: #000080;">--normalize</span> <span class="nt" style="color: #000080;">--defaultprior</span> <span class="nt" style="color: #000080;">--select</span> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"8. Testing Bayesian model selection (empirical prior)..."</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">trinculo multinom <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Pheno <span class="nt" style="color: #000080;">--basepheno</span> Control <span class="nt" style="color: #000080;">--covar</span> pcs.txt <span class="nt" style="color: #000080;">--normalize</span> <span class="nt" style="color: #000080;">--empiricalprior</span> <span class="nt" style="color: #000080;">--select</span> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"9. Testing ordinal regression..."</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell">trinculo ordinal <span class="nt" style="color: #000080;">--bfile</span> genotypes <span class="nt" style="color: #000080;">--pheno</span> phenos.txt <span class="nt" style="color: #000080;">--phenoname</span> Order <span class="nt" style="color: #000080;">--covar</span> pcs.txt</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASSED"</span></span></pre>
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