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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pftools">Debian Med / pftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/95486f8f48f471184680851920597ceb3d4c0170">95486f8f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-25T09:58:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use Github tags instead of releases
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/faba900e77f2f8cd41f2b573e15ba98156e32cf3">faba900e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-25T09:58:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/3ea320c1dac134178ce64762c5e234db51c0ee15">3ea320c1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-25T09:58:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.11</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/ea8c056443e44db59bab95a56f84dab63dce24ab">ea8c0564</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-25T10:00:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.11'
Update to upstream version '3.2.11'
with Debian dir d33db93b0ad677add8a637a11624b74f19587bd2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/4a13523419c3be98eced4804875436eb9b992d0b">4a135234</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-25T10:01:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing build dependency on dh addon.
Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/27db68c33cfd5e2c69149eaf52fc7169cab72e12">27db68c3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-25T10:05:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#59e70f737a878c10c711a056493a7d58029945cc">
Docker/README.docker
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
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<li class="file-stats">
<a href="#33a08aca934f37c2d0beb1888a2a6794fe9b0219">
src/C/config.h.cmake
</a>
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<li class="file-stats">
<a href="#edc76d1689c1a7f0bd0401f05fd6b05ea7f6e15b">
tests/examples/test_V3.sh.cmake
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</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">build/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">testing/</span>
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<td class="new_line diff-line-num" data-linenumber="3" 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="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="4" 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="LC4" class="line" lang="plaintext">\.kdev4/</span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<br>
</li>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># PfTools versioning</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>VERSION <span class="s2" style="color: #d14;">"3.2.<span class="idiff left right">8</span>"</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="4" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>VERSION <span class="s2" style="color: #d14;">"3.2.<span class="idiff left right">11</span>"</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="5" 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">
5
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<td class="new_line diff-line-num" data-linenumber="5" 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">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>MAJOR_VERSION <span class="s2" style="color: #d14;">"3"</span><span class="p">)</span></span>
</pre>
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6
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<td class="new_line diff-line-num" data-linenumber="6" 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="LC6" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>MINOR_VERSION <span class="s2" style="color: #d14;">"2"</span><span class="p">)</span></span>
</pre>
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7
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<td class="new_line diff-line-num old" data-linenumber="7" 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="LC7" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>PATCH_VERSION <span class="s2" style="color: #d14;">"<span class="idiff left right">8</span>"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>PATCH_VERSION <span class="s2" style="color: #d14;">"<span class="idiff left right">11</span>"</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="8" 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="LC8" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>DATA_PATH <span class="s2" style="color: #d14;">"share/data"</span> CACHE STRING <span class="s2" style="color: #d14;">"Installation data folder"</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="9" 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">
9
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<td class="new_line diff-line-num" data-linenumber="9" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>DOC_PATH <span class="s2" style="color: #d14;">"share/doc"</span> CACHE STRING <span class="s2" style="color: #d14;">"Installation doc folder"</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="10" 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">
10
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<td class="new_line diff-line-num" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>MAN1_PATH <span class="s2" style="color: #d14;">"share/man/man1"</span> CACHE STRING <span class="s2" style="color: #d14;">"Installation man1 folder"</span> <span class="p">)</span></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">@@ -396,7 +396,7 @@ ADD_SUBDIRECTORY(data)</td>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Enabling TESTING</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CTest<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>TESTS_DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/<span class="idiff left">T</span>est<span class="idiff right">s</span>"</span> CACHE PATH <span class="s2" style="color: #d14;">"Directory for tests"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>TESTS_DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/<span class="idiff left">t</span>est<span class="idiff right">ing</span>"</span> CACHE PATH <span class="s2" style="color: #d14;">"Directory for tests"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>TESTS_DATA_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/tests"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>NOT EXISTS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">TESTS_DIRECTORY</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FILE</span><span class="p">(</span>MAKE_DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">TESTS_DIRECTORY</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#59e70f737a878c10c711a056493a7d58029945cc"><strong>Docker/README.docker</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Build Docker image</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="docker">export PFTOOLS_VERSION=3.2.<span class="idiff left right">6</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker">export PFTOOLS_VERSION=3.2.<span class="idiff left right">11</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker">docker build -t pftools:$PFTOOLS_VERSION --no-cache=true --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg PFTOOLS_VERSION=$PFTOOLS_VERSION -f Dockerfile . 2>&1 >pftools.Dockerfile.log</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="docker"></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># PfTools v3.2</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/pftools/README.html)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda-Server Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/pftools/badges/license.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/pftools)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda-Server Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/pftools.svg?style=flat</span><span class="p">)</span>](https://anaconda.org/bioconda/pftools)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">PfTools</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=========================================</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Table of Contents</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Foreword</span><span class="p">](</span><span class="sx" style="color: #d14;">#foreword</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Using Docker</span><span class="p">](</span><span class="sx" style="color: #d14;">#using-docker</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Using Singularity</span><span class="p">](</span><span class="sx" style="color: #d14;">#using-singularity</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">#bioconda</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Manually</span><span class="p">](</span><span class="sx" style="color: #d14;">#manually</span><span class="p">)</span> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Generalized profile syntax</span><span class="p">](</span><span class="sx" style="color: #d14;">#generalized-profile-syntax</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Algorithms description</span><span class="p">](</span><span class="sx" style="color: #d14;">#algorithms-description</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Applications of the Pftools</span><span class="p">](</span><span class="sx" style="color: #d14;">#applications-of-the-pftools</span><span class="p">)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Authors</span><span class="p">](</span><span class="sx" style="color: #d14;">#authors</span><span class="p">)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Foreword</span></span>
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2
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown">(C) Copyright SIB Swiss Institute of Bioinformatics</span>
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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">available from https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +27,86 @@ available from https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.</td>
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7
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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">Version 3 contains the original FORTRAN 77 pftools (release 2.3)</span>
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<td class="old_line diff-line-num" data-linenumber="8" 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">
8
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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">and the new pftoolsV3 programs.</span>
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<td class="old_line diff-line-num" data-linenumber="9" 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="new_line diff-line-num" 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="markdown"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">The 'pftools' package documententation is unfortunately scattered over many</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">different places. Here is an annotated list of the relevant documents we are</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">aware of:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Installation</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using Docker</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">First you must have <span class="p">[</span><span class="nv" style="color: #008080;">Docker</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.docker.com/get-docker/</span><span class="p">)</span> installed and running. </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">Secondly have a look at the availabe pftools biocontainers at <span class="p">[</span><span class="nv" style="color: #008080;">quay.io</span><span class="p">](</span><span class="sx" style="color: #d14;">https://quay.io/repository/biocontainers/pftools?tab=tags</span><span class="p">)</span> or at <span class="p">[</span><span class="nv" style="color: #008080;">Docker Hub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/sibswiss/pftools</span><span class="p">)</span>. </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">Then:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"> <span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"># get the chosen pftools container version</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown">docker pull quay.io/biocontainers/pftools:2.3.5--h4333106_0</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"> or</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown">docker pull sibswiss/pftools:3.2.8</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"># use an pftools's tool e.g. pfscan </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">docker run quay.io/biocontainers/pftools:2.3.5--h4333106_0 pfscan -h</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"> or</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown">docker run sibswiss/pftools:3.2.8 pfscan -h</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"> <span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using Singularity</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">First you must have <span class="p">[</span><span class="nv" style="color: #008080;">Singularity</span><span class="p">](</span><span class="sx" style="color: #d14;">https://sylabs.io/guides/master/user-guide/quick_start.html</span><span class="p">)</span> installed and running.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown">Secondly have a look at the availabe pftools biocontainers at <span class="p">[</span><span class="nv" style="color: #008080;">quay.io</span><span class="p">](</span><span class="sx" style="color: #d14;">https://quay.io/repository/biocontainers/pftools?tab=tags</span><span class="p">)</span> or at <span class="p">[</span><span class="nv" style="color: #008080;">Docker Hub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/sibswiss/pftools</span><span class="p">)</span>. </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">Then:</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">```</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"># get the chosen pftools container version</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">singularity pull docker://quay.io/biocontainers/quay.io/biocontainers/pftools:2.3.5--h4333106_0</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"> or</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">singularity pull docker://sibswiss/pftools:3.2.8</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"># run the container</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">singularity run pftools_2.3.5--h4333106_0.sif</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="p">```</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">You are now in the container. You can use an pftools's tool e.g. pfscan doing </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="p">```</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">pfscan -h</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="p">```</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Bioconda</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">```</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown">conda install -c bioconda pftools</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="p">```</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Manually</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown">See <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">./INSTALL</span><span class="p">)</span> for more information</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Prerequisite**</span> </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="p"> *</span> cmake >= 3.7</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p"> *</span> gcc >= 4.6</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="p"> *</span> gfortran (or g77 or f77) for release 2.3 source code</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="p"> *</span> perl >= 5.5.3 </span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="p"> *</span> File::Slurp</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**BUILD**</span> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="p">```</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown">git clone https://github.com/sib-swiss/pftools3.git</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown">cd pftools3</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">mkdir build</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown">cd build/</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">cmake ..</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="p">```</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**COMPILE**</span> </span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="p">```</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown">make</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="p">```</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"></span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**INSTALL**</span> </span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown">make install</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**CHECK/TEST**</span> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown">make test</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="p">```</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown">After installation, in the share/examples/ subdirectory, the <span class="ge" style="font-style: italic;">*test_V3.sh*</span> shell script is a good starting point for using pfsearchV3/pfscanV3.</span>
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13
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>
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14
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Generalized profile syntax</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" 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">@@ -27,10 +124,6 @@ it was originally published in</td>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"> PubMed PMID: <span class="p">[</span><span class="nv" style="color: #008080;">7584418</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/pubmed/7584418</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Command-line tutorial</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">After installation, in the share/examples/ subdirectory, the <span class="ge" style="font-style: italic;">*test_V3.sh*</span> shell script is a good starting point for using pfsearchV3/pfscanV3.</span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"></span>
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34
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Algorithms description</span></span>
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35
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"></span>
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36
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown">Technical details about how profiles can be constructed and parametrized</span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pftools (3.2.11-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use Github tags instead of releases</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add missing build dependency on dh addon.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 25 Jan 2022 10:01:51 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">pftools (3.2.8-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#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">@@ -9,7 +9,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libfile-slurp-perl,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libreadline-dev,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> debhelper</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pftools</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pftools.git</span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/sib-swiss/pftools3/<span class="idiff left right">/release</span>s .*/v?@ANY_VERSION@\.tar\.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/sib-swiss/pftools3/<span class="idiff left right">tag</span>s .*/v?@ANY_VERSION@\.tar\.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#33a08aca934f37c2d0beb1888a2a6794fe9b0219"><strong>src/C/config.h.cmake</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">@@ -10,11 +10,9 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#define __USE_WINAPI__</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#cmakedefine USE_AFFINITY</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#if defined(USE_AFFINITY)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># if defined(__GNUC__) && !defined(USE_WINAPI)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># define _GNU_SOURCE</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># endif</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake">/* NOTE Compilation fails if _GNU_SOURCE is not defined with affinity off */</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#if defined(__GNUC__) && !defined(USE_WINAPI)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># define _GNU_SOURCE</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cmake">/*</span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/98eac2308923a27ba42a122b5d07ae779958a8d8...27db68c33cfd5e2c69149eaf52fc7169cab72e12#edc76d1689c1a7f0bd0401f05fd6b05ea7f6e15b"><strong>tests/examples/test_V3.sh.cmake</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" 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>
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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">@@ -127,11 +127,11 @@ $PFSCANV3 -n -t 1 -q ./hiv.prf ./hiv.fastq # FASTQ</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Default output mode:</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cmake">$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.2.hit</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cmake">$PFSEARCH <span class="idiff left right"> </span>-f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.2.hit</span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cmake">$PFSEARCHV3 -n -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.3.hit</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cmake">diff -b $TMPDIR/sh3.VAV_HUMAN.2.hit $TMPDIR/sh3.VAV_HUMAN.3.hit <span class="c1" style="color: #998; font-style: italic;"># expecting no difference</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cmake">$PFSEARCH -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.2.hit</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cmake">$PFSEARCH <span class="idiff left right"> </span>-fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.2.hit</span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cmake">$PFSEARCHV3 -n -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.3.hit</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cmake">diff -b $TMPDIR/ecp.CVPBR322.2.hit $TMPDIR/ecp.CVPBR322.3.hit <span class="c1" style="color: #998; font-style: italic;"># expecting no difference</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cmake"></span>
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