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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pique">Debian Med / pique</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/fb07dcae88e7d383987f910d8515edc9d4fb457c">fb07dcae</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T12:50:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/6cbd89818e8b3aa0284f112056721dea4574ba71">6cbd8981</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T13:44:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/5a32daea391616e6a6a66a0b394a8b92707d2745">5a32daea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T13:49:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">create extra doc package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/cb0d0d34ece1327140d549b8976400b4d72e68d5">cb0d0d34</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T13:58:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Script should somehow work as autopkgtest but its not activated for the moment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/0dd6cdbc09323fd9b57915dbb5eb23d106405c8b">0dd6cdbc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T14:01:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix description
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="deleted-file">
−
debian/docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#f0d2b4c11cf7c18c7abc1fbb1fb4da4cb0680fcb">
<span class="new-file">
+
debian/pique-doc.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#37e054b2fbccd5d1d2afadbffd92a5f4f043bb0d">
<span class="new-file">
+
debian/pique-input.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#8f9c1142f579b9e9f3606ab62877f512f5e7fa64">
<span class="new-file">
+
debian/pique-run.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#67dc024aafc279282bbb7fe85149987781e892a4">
debian/install
→
debian/pique.install
</a>
</li>
<li class="file-stats">
<a href="#d7534fe85f3c54c109b5ec7e062e991adeabb489">
<span class="new-file">
+
debian/pique.manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" 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">@@ -21,7 +21,9 @@ Depends: ${perl:Depends},</td>
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<td class="diff-line-num new_line" data-linenumber="21" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libreadonly-perl,</span>
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<td class="diff-line-num old_line" data-linenumber="22" 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">
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<td class="diff-line-num new_line" data-linenumber="22" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> libparallel-forkmanager-perl,</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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">
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<td class="diff-line-num new_line" data-linenumber="23" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libfile-slurp-perl,</span>
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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> r-cran-getopt,</span>
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<td class="diff-line-num old_line" data-linenumber="24" 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">
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<td class="diff-line-num new_line" data-linenumber="25" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> r-cran-forecast,</span>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> r-cran-optparse,</span>
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<td class="diff-line-num old_line" data-linenumber="25" 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">
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<td class="diff-line-num new_line" data-linenumber="27" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> r-cran-uroot</span>
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<td class="diff-line-num old_line" data-linenumber="26" 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">
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<td class="diff-line-num new_line" data-linenumber="28" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Description: software pipeline for performing genome wide association studies</span>
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<td class="diff-line-num old_line" data-linenumber="27" 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">
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<td class="diff-line-num new_line" data-linenumber="29" 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">
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> PIQUE is a software pipeline for performing genome wide association</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="35" 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">@@ -33,10 +35,35 @@ Description: software pipeline for performing genome wide association studies</td>
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<td class="diff-line-num new_line" data-linenumber="35" 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">
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> running EMMAX, ensuring that the various input data files are in the</span>
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<td class="diff-line-num old_line" data-linenumber="34" 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">
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<td class="diff-line-num new_line" data-linenumber="36" 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">
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> correct format. PIQUE proceeds in two main stages although there are</span>
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<td class="diff-line-num new_line" data-linenumber="37" 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">
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> multiple entry and exit points from which the pipeline can be run. The</span>
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<td class="diff-line-num new_line old" data-linenumber="38" 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="LC36" class="line" lang="plaintext"> first stage consists of running the “<span class="idiff left right">emmax</span>-input” program, which can</span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> first stage consists of running the “<span class="idiff left right">pique</span>-input” program, which can</span>
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<td class="diff-line-num new_line" data-linenumber="39" 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">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> read genotype and phenotype information in several different formats and</span>
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<td class="diff-line-num new_line" data-linenumber="40" 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">
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> generates all the necessary input files required to run EMMAX. The</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> second step in the pipeline uses the “<span class="idiff left right">emmax</span>-run” program to actually run</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> EMMAX using the files generated by “<span class="idiff left right">emmax</span>-input” (or pre-existing</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> second step in the pipeline uses the “<span class="idiff left right">pique</span>-run” program to actually run</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> EMMAX using the files generated by “<span class="idiff left right">pique</span>-input” (or pre-existing</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> user-supplied input files) to perform the GWAS and output the analysis</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> summary files.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Package: pique-doc</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Section: doc</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Enhances: pique</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Description: software pipeline for performing genome wide association studies (docs)</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> PIQUE is a software pipeline for performing genome wide association</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> studies (GWAS). The main function of PIQUE is to provide ‘convenience’</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> wrappers that allow users to perform GWAS using the popular program</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> EMMAX (Kang et al., 2010) without the need to be familiar with all of</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> the software tools used to generate the required EMMAX input files.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> PIQUE will also perform a number of quality control steps prior to</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> running EMMAX, ensuring that the various input data files are in the</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> correct format. PIQUE proceeds in two main stages although there are</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> multiple entry and exit points from which the pipeline can be run. The</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> first stage consists of running the “pique-input” program, which can</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> read genotype and phenotype information in several different formats and</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> generates all the necessary input files required to run EMMAX. The</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> second step in the pipeline uses the “pique-run” program to actually run</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> EMMAX using the files generated by “pique-input” (or pre-existing</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> user-supplied input files) to perform the GWAS and output the analysis</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> summary files.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> .</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> This package contains the documentation as well as example data.</span></pre>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>pique-input</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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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="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>pique-run</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</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="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">doc/*.odt</span></pre>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#f0d2b4c11cf7c18c7abc1fbb1fb4da4cb0680fcb"><strong>debian/pique-doc.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">doc</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">odt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">pique</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">pique</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#37e054b2fbccd5d1d2afadbffd92a5f4f043bb0d"><strong>debian/pique-input.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PIQUE-INPUT "1" "July 2020" "pique-input 1.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">pique-input \- software pipeline for performing genome wide association studies</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B pique</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,-i in_prefix -o out_prefix\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-d] [\-v] [\-f in_format] [\-k kinship]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-p pheno_file] [\-c covar_file [\-e n_pc]]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS Mandatory parameters:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-i\fR in_prefix: input prefix for the input files</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-o\fR out_prefix: output prefix for the output files</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS Optional parameters:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-d\fR debug: saves intermediate files for debugging</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-v\fR verbose: display all output from plink and smartpca</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-f\fR in_format: input file format (default = ped)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">ped = requires in_prefix.ped & in_prefix.map files</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">tped = requires in_prefix.tped & in_prefix.tfam files</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">vcf = requires .vcf filename</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-p\fR pheno_file: phenotype file name</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Defaults to [in_prefix].pheno</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.HP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-g\fR group[,group...]: genotype sub\-groups to be analysed</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-n\fR number: minimum number of genotypes in sub\-group (default = 20)</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-k\fR kinship: method to calculate kinship matrix</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Either 'IBS' (default) or 'BN' methods</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-c\fR covar_file: generate covariate file [out_prefix].covar</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">from SNP information in .ped file using smartpca (EIGENSOFT)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-e\fR n_pc: number of eigenvectors to keep from smartpca</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-m\fR MAF: Minor Allele Frequency</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-x\fR missing: maximum per\-SNP missing</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Further details and examples are given in the documentation</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Tony Travis <tony.travis@abdn.ac.uk> and Alex Douglas <a.douglas@abdn.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">can be used for any other usage of the program.</span></pre>
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<li id="8f9c1142f579b9e9f3606ab62877f512f5e7fa64">
<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#8f9c1142f579b9e9f3606ab62877f512f5e7fa64"><strong>debian/pique-run.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PIQUE-RUN "1" "July 2020" "pique-run 1.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">pique-run \- software pipeline for performing genome wide association studies</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B pique-run</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,-i in_prefix \/\fR[\fI\,-n threads\/\fR] [\fI\,-o out_prefix\/\fR] [\fI\,-k kinship\/\fR] [\fI\,-c cov_file\/\fR] \fI\,-t transform\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS Mandatory parameters:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-i\fR in_prefix: input prefix for .tped .tfam and .pheno files</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SS Optional parameters:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-n\fR threads: number of threads. Defaults to 1</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-o\fR out_prefix: prefix for output files. Defaults to [input_prefix]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-k\fR kinship: method used to calculate kinship matrix. Either 'IBS' (default) or 'BN' methods</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-c\fR cov_file: covariate file name</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-t\fR transform: phenotype transformation (BC = Box\-Cox, default = none)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">More information about pique\-run usage can be found in the PIQUE documentation</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Tony Travis <tony.travis@abdn.ac.uk> and Alex Douglas <a.douglas@abdn.ac.uk</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#67dc024aafc279282bbb7fe85149987781e892a4"><strong>debian/install</strong>
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<strong>debian/pique.install</strong>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#d7534fe85f3c54c109b5ec7e062e991adeabb489"><strong>debian/pique.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/pique/-/compare/701abe3a36c77e2a9b513b5817cb33f360f01f8d...0dd6cdbc09323fd9b57915dbb5eb23d106405c8b#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">pique</span></span>
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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="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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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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">@@ -15,4 +12,4 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC13" 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="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#do_stuff_to_test_package#</span></span></span></pre>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="idiff left right">make</span></span></pre>
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