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<h3>
Shayan Doust pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/covtobed">Debian Med / covtobed</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5">78e1536e</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-02T18:41:45+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.2+dfsg</pre>
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<h4>10 changed files:</h4>
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Docker/README.md
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Docker/coverage
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Docker/v2.3.0.tar.gz
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binaries/README.md
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binaries/build_osx.sh
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binaries/build_ubuntu.sh
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binaries/covtobed
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binaries/covtobed_debug
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binaries/covtobed_mac
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binaries/covtobed_mac_debug
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<h4>Changes:</h4>
<li id="b6ce619255b7ed6731c8b6f6a057e5fde57c1b8f">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5#b6ce619255b7ed6731c8b6f6a057e5fde57c1b8f"><strong>Docker/README.md</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Docker container</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown">This directories contains files to generate the Docker/Singularity images that provide:</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`covtobed`</span> as described in the <span class="p">[</span><span class="nv" style="color: #008080;">README</span><span class="p">](</span><span class="sx" style="color: #d14;">../README.md</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`coverage`</span> a legacy program with some more features that has been used for the EU project _MD-PAEDIGREE_.</span>
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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;">## How to get it</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">The Docker image is distributed via <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/andreatelatin/covtobed</span><span class="p">)</span>:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>docker pull andreatelatin/covtobed</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">The Singularity image can be pulled from Docker Hub as well. A snapshot (v. 0.3) is available from <span class="p">[</span><span class="nv" style="color: #008080;">Zenodo</span><span class="p">](</span><span class="sx" style="color: #d14;">https://zenodo.org/record/1063493</span><span class="p">)</span>:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">singularity pull andreatelatin/covtobed</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"><span class="p">```</span></span></pre>
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<li id="4f81671e3b6e5635980fd6f753749340b1380d63">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5#4f81671e3b6e5635980fd6f753749340b1380d63"><strong>Docker/coverage</strong>
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<li id="0e0ec51dac7273af212f79be5eae5689698cd288">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5#0e0ec51dac7273af212f79be5eae5689698cd288"><strong>Docker/v2.3.0.tar.gz</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Precompiled binaries for Linux and OS X</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">*</span> Linux: <span class="p">[</span><span class="nv" style="color: #008080;">https://github.com/telatin/covtobed/releases/download/v0.3/covtobed</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/telatin/covtobed/releases/download/v0.3/covtobed</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">*</span> OS X: <span class="p">[</span><span class="nv" style="color: #008080;">https://github.com/telatin/covtobed/releases/download/v0.3/covtobed_osx</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/telatin/covtobed/releases/download/v0.3/covtobed_osx</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">The Linux binary has been tested with Ubuntu 14.04, Ubuntu 18.04, Fedora 26 and Fedora 30.</span></pre>
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<a href="https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5#188d80b3be933d6a1fcf50e4ad59a1d2c30ab721"><strong>binaries/build_osx.sh</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">/miniconda3"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"MINICONDA not found in </span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">/miniconda3"</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">/miniconda3/lib/libbamtools.a"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"'</span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">/miniconda3/lib/libbamtools.a' not found"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>2<span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-euxo</span> pipefail</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">SCRIPT_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASH_SOURCE</span><span class="p">[0]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>/dev/null <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SCRIPT_DIR</span><span class="s2" style="color: #d14;">/.."</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span>.bak <span class="s1" style="color: #d14;">'s/#define debug if(.*)/#define debug if(true)/'</span> base.cpp</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">c++ <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 ./<span class="k" style="font-weight: 600;">*</span>.cpp <span class="nt" style="color: #000080;">-I</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/miniconda3/include/bamtools/ <span class="nt" style="color: #000080;">-L</span><span class="s2" style="color: #d14;">$"{HOME}"</span>/miniconda3/lib/ <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">"</span>/miniconda3/lib/libbamtools.a <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> binaries/covtobed_mac_debug <span class="nt" style="color: #000080;">-lz</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span>.bak <span class="s1" style="color: #d14;">'s/#define debug if(.*)/#define debug if(false)/'</span> base.cpp</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">c++ <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 ./<span class="k" style="font-weight: 600;">*</span>.cpp <span class="nt" style="color: #000080;">-I</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/miniconda3/include/bamtools/ <span class="nt" style="color: #000080;">-L</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/miniconda3/lib/ <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$HOME</span><span class="s2" style="color: #d14;">"</span>/miniconda3/lib/libbamtools.a <span class="se" style="color: #d14;">\</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> binaries/covtobed_mac <span class="nt" style="color: #000080;">-lz</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> -</span></pre>
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<li id="784889c9ad1b96d7ecd451d0a873c45b790205a3">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/78e1536e9f995a857dc3eeeb05027c5dacc594b5#784889c9ad1b96d7ecd451d0a873c45b790205a3"><strong>binaries/build_ubuntu.sh</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-euxo</span> pipefail</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">SCRIPT_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASH_SOURCE</span><span class="p">[0]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>/dev/null <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SCRIPT_DIR</span><span class="s2" style="color: #d14;">/.."</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Make DEBUG</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s1" style="color: #d14;">'s/#define debug if(.*)/#define debug if(true)/'</span> base.cpp</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell">c++ <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 ./<span class="k" style="font-weight: 600;">*</span>.cpp <span class="nt" style="color: #000080;">-I</span>/usr/include/bamtools /usr/lib/x86_64-linux-gnu/libbamtools.a /usr/lib/gcc/x86_64-linux-gnu/5/libstdc++.a <span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> binaries/covtobed_debug <span class="nt" style="color: #000080;">-lz</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Make NORMAL</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s1" style="color: #d14;">'s/#define debug if(.*)/#define debug if(false)/'</span> base.cpp</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">c++ <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 ./<span class="k" style="font-weight: 600;">*</span>.cpp <span class="nt" style="color: #000080;">-I</span>/usr/include/bamtools /usr/lib/x86_64-linux-gnu/libbamtools.a /usr/lib/gcc/x86_64-linux-gnu/5/libstdc++.a <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> binaries/covtobed <span class="nt" style="color: #000080;">-lz</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> -</span></pre>
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