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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/tiddit">Debian Med / tiddit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/ddf32d81524cb7f84f3288a9db40a2e04c36f4c4">ddf32d81</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-04T01:31:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/watch: Fix watch regex
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/dd8fe12d3be8d99d50569eeb3d072f9e52177bc3">dd8fe12d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-04T01:31:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.12.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/4cb83ad405aea4a8f501201efb413d708f430143">4cb83ad4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-04T01:31:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.12.1+dfsg'
Update to upstream version '2.12.1+dfsg'
with Debian dir 5aef6248749e72b7c0c872520900049984fc2849</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/d3049902cb71958081ef9759209fe15b1e22d70f">d3049902</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-04T01:33:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/e4bdf4c1cb193eee4903560e3e2dbec169c08bd6">e4bdf4c1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-06-04T01:39:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<span class="new-file">
+
Dockerfile
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</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#2ff2722d014ed036cd63fac102a8a8d03276bc4e">
TIDDIT.py
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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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
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<li class="file-stats">
<a href="#b6c83ca2a4ea6b793cb00a89dd01be5a17651ec0">
src/TIDDIT.cpp
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<li class="file-stats">
<a href="#8408f176d0a82d41f475e43ca2a03af2c28d437e">
<span class="new-file">
+
versioned_singularity/TIDDIT.2.12.1
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</a>
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</ul>
<h4>Changes:</h4>
<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> python:3.8-slim</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="docker"> apt-get upgrade <span class="nt" style="color: #000080;">-y</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" 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="LC5" class="line" lang="docker"> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" 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="LC6" class="line" lang="docker"> autoconf <span class="se" style="color: #d14;">\</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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker"> automake <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="docker"> build-essential <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="docker"> cmake <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="docker"> libbz2-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker"> libcurl4-gnutls-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"> liblzma-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="docker"> libncurses5-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"> libssl-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker"> make <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="docker"> unzip <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="docker"> wget <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="docker"> zlib1g-dev <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"> apt-get clean <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"> apt-get purge <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> /var/lib/apt/lists/<span class="k" style="font-weight: 600;">*</span> /tmp/<span class="k" style="font-weight: 600;">*</span> /var/tmp/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="docker"><span class="k" style="font-weight: 600;">WORKDIR</span><span class="s" style="color: #d14;"> /app</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">## Install samtools for cram processing</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>wget <span class="nt" style="color: #000080;">--no-verbose</span> https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="docker"> bunzip2 samtools-1.10.tar.bz2 <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xf</span> samtools-1.10.tar <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">cd </span>samtools-1.10 <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="docker"> ./configure <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="docker"> make all all-htslib <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="docker"> make <span class="nb" style="color: #0086b3;">install </span>install-htslib <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">rm</span> /app/samtools-1.10.tar</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">## Set TIDDIT version</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> TIDDIT_VERSION=2.12.0</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">## Add some info</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> base_image="python:3.8-slim"</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> software="TIDDIT.py"</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> software.version=${TIDDIT_VERSION}</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">## Download and extract</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TIDDIT_VERSION</span><span class="k" style="font-weight: 600;">}</span>.zip <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="docker"> unzip TIDDIT-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TIDDIT_VERSION</span><span class="k" style="font-weight: 600;">}</span>.zip <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">rm </span>TIDDIT-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TIDDIT_VERSION</span><span class="k" style="font-weight: 600;">}</span>.zip</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">## Install</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">cd </span>TIDDIT-TIDDIT-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TIDDIT_VERSION</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="docker"> ./INSTALL.sh <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">chmod</span> +x /app/TIDDIT-TIDDIT-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TIDDIT_VERSION</span><span class="k" style="font-weight: 600;">}</span>/TIDDIT.py <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> /app/TIDDIT-TIDDIT-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TIDDIT_VERSION</span><span class="k" style="font-weight: 600;">}</span>/TIDDIT.py /usr/local/bin </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENTRYPOINT</span><span class="s" style="color: #d14;"> ["TIDDIT.py"]</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="docker"><span class="k" style="font-weight: 600;">CMD</span><span class="s" style="color: #d14;"> ["--help"]</span></span></pre>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -83,28 +83,56 @@ The reference is required for analysing cram files.</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">NOTE: It is important that you use the TIDDIT.py wrapper for SV detection. The TIDDIT binary in the TIDDIT/bin folder does not perform any clustering, it simply extract SV signatures into a tab file.</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown">TIDDIT may be fine tuned by altering these optional parameters:</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o - The prefix of the output files(default = output)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -i - The maximum allowed insert size of a normal pair. Pairs having larger insert </span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;"> than this is treated as discordant pairs. Default is 99.9th percentile + 100 bp</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -d - The pair orientation, use this setting to override the automatic orientation selection</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -l - The density parameter, to create a cluster, more than l signals (split reads+ discordant pairs) must be present, signals are added to a cluster if they are neighbouring atleast this number of signals (defualt 3, minimum 2)</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -p - The minimum number of discordant pairs and supplementary alignments used to call large SV. Default is 3</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -r - The minimum number of supplementary alignments used to call small SV. Default is 3</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -q - The minimum mapping quality of the discordant pairs/supplementary alignments </span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown"><span class="sb" style="color: #d14;"> forming a variant. Default value is 5.</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -n - The ploidy of the organism ,(default = 2)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown">TIDDIT may be fine-tuned by altering these optional parameters:</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o output prefix(default=output)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -i paired reads maximum allowed insert size. Pairs aligning</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="sb" style="color: #d14;"> on the same chr at a distance higher than this are</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="sb" style="color: #d14;"> considered candidates for SV (default= 99.9th percentile of insert size)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -d expected reads orientations, possible values "innie" (-> <-) or "outtie" (<- ->). </span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Default: major orientation within the dataset</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -p Minimum number of supporting pairs in order to call a variation event (default 3)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -r Minimum number of supporting split reads to call a small variant (default 3)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -q Minimum mapping quality to consider an alignment (default= 5)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -Q Minimum regional mapping quality (default 20)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -n the ploidy of the organism,(default = 2)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -e clustering distance parameter, discordant pairs closer</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="sb" style="color: #d14;"> than this distance are considered to belong to the same</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="sb" style="color: #d14;"> variant(default = sqrt(insert-size*2)*12)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -l min-pts parameter (default=3),must be set >= 2</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -s Number of reads to sample when computing library statistics(default=25000000)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -z minimum variant size (default=100), variants smaller than</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="sb" style="color: #d14;"> this will not be printed ( z < 10 is not recomended)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --force_ploidy force the ploidy to be set to -n across the entire genome</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"><span class="sb" style="color: #d14;"> (i.e skip coverage normalisation of chromosomes)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --no_cluster Run only the TIDDIT signal extraction</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --debug rerun the tiddit clustering procedure</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --n_mask exclude regions from coverage calculation if they contain more than this fraction of N (default = 0.5)</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --ref reference fasta, used for GC correction and for reading cram</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --p_ratio minimum discordant pair/normal pair ratio at the breakpoint junction(default=0.2)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --r_ratio minimum split read/coverage ratio at the breakpoint junction(default=0.1)</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --force_ploidy - set the ploidy of all chromosomes to -n (including the sex chromosomes), this option will disable the ploidy estimation.</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="sb" style="color: #d14;"> This option is meant to be used for low quality data or for species having equal ploidy across all chromosomes</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown">output:</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"></span>
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<li id="2ff2722d014ed036cd63fac102a8a8d03276bc4e">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#2ff2722d014ed036cd63fac102a8a8d03276bc4e"><strong>TIDDIT.py</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">@@ -8,7 +8,7 @@ wd=os.path.dirname(os.path.realpath(__file__))</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'{}/src/'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">wd</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">TIDDIT_calling</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.12.<span class="idiff left right">0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.12.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="s" style="color: #d14;">"""TIDDIT-{}"""</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">),</span><span class="n" style="color: #333;">add_help</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sv'</span> <span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"call structural variation"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--cov'</span> <span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"generate a coverage bed file"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</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">@@ -35,8 +35,8 @@ if args.sv:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--debug'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rerun the tiddit clustering procedure"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--n_mask'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exclude regions from coverage calculation if they contain more than this fraction of N (default = 0.5)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--ref'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"reference fasta, used for GC correction and for reading cram"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--p_ratio'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minimum discordant pair/normal pair ratio at the breakpoint junction(default=<span class="idiff left right">20%</span>)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--r_ratio'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minimum split read/coverage ratio at the breakpoint junction(default=<span class="idiff left right">10%</span>)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--p_ratio'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minimum discordant pair/normal pair ratio at the breakpoint junction(default=<span class="idiff left right">0.2</span>)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--r_ratio'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minimum split read/coverage ratio at the breakpoint junction(default=<span class="idiff left right">0.1</span>)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">wd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tiddit (2.12.1+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Update metadata - added ref to bio.tools</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"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * d/watch: Fix watch regex</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * New upstream version 2.12.1+dfsg</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Declare compliance with policy 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Fri, 04 Jun 2021 01:33:49 +0530</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">tiddit (2.12.0+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#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">@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libbamtools-dev (>= 2.5.1+dfsg-6),</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">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tiddit</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tiddit.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/SciLifeLab/TIDDIT</span>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#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="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,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/SciLifeLab/TIDDIT/releases .*/archive/TIDDIT-@ANY_VERSION@\.tar\.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">https://github.com/SciLifeLab/TIDDIT/releases .*/archive/<span class="idiff left right">.*/</span>TIDDIT-@ANY_VERSION@\.tar\.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#b6c83ca2a4ea6b793cb00a89dd01be5a17651ec0"><strong>src/TIDDIT.cpp</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">@@ -46,7 +46,7 @@ int main(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_variant_size</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000000</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">outputFileHeader</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"output"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.12.<span class="idiff left right">0</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.12.<span class="idiff left right">1</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//collect all options as a vector</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">arguments</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">argc</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/tiddit/-/compare/1337afa9fab96ad438a3b7cd88a46e17101f756e...e4bdf4c1cb193eee4903560e3e2dbec169c08bd6#8408f176d0a82d41f475e43ca2a03af2c28d437e"><strong>versioned_singularity/TIDDIT.2.12.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">BootStrap: debootstrap</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">OSVersion: trusty</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">MirrorURL: http://us.archive.ubuntu.com/ubuntu/</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">%runscript</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> echo "This is what happens when you run the container..."</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">%post</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> echo "Hello from inside the container"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> sed -i 's/$/ universe/' /etc/apt/sources.list</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> apt-get update</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget libbz2-dev unzip</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> easy_install pip</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> pip install numpy cython</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.1.zip</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> unzip TIDDIT-2.12.1.zip</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> mv TIDDIT-TIDDIT-2.12.1/* /bin/</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> cd /bin/ && ./INSTALL.sh</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> chmod +x /bin/TIDDIT.py</span></pre>
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