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<h3>
Aikaterini Kalou pushed to branch master
at <a href="https://salsa.debian.org/med-team/macs">Debian Med / macs</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357">2cc4ef8c</a></strong>
<div>
<span>by kkalou-guest</span>
<i>at 2018-02-19T00:14:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added a new test directory for autopkgtest along with some sample data
</pre>
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<h4>7 changed files:</h4>
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README.test
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debian/examples/aluY.chr1.bed
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debian/examples/gerp.chr1.bed
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debian/macs-example-data.install
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debian/macs.examples
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debian/tests/control
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9d3024ca52a502f93c1a872832cfdf2da3a5e487">
<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#9d3024ca52a502f93c1a872832cfdf2da3a5e487"><strong>README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">otes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" 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="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">executing</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="php"><span class="nx">Notes</span> <span class="o" style="font-weight: 600;">:</span> <span class="nx">the</span> <span class="nx">sample</span> <span class="nx">data</span> <span class="nx">are</span> <span class="nx">recovered</span> <span class="nx">from</span><span class="p">;</span> <span class="nx">https</span><span class="o" style="font-weight: 600;">://</span><span class="nx">github</span><span class="o" style="font-weight: 600;">.</span><span class="nx">com</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arq5x</span><span class="o" style="font-weight: 600;">/</span> <span class="nx">They</span> <span class="nx">are</span> <span class="nx">both</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">‘</span><span class="o" style="font-weight: 600;">.</span><span class="nx">BED</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">’</span> </span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"><span class="nb" style="color: #0086b3;">file</span> <span class="nx">extensions</span><span class="o" style="font-weight: 600;">.</span> <span class="nx">However</span> <span class="nx">the</span> <span class="nx">macs</span> <span class="nx">package</span> <span class="nx">install</span> <span class="nx">instructions</span> <span class="nx">is</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"><span class="nx">using</span> <span class="nx">the</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">‘</span><span class="nx">BAM</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">’</span> <span class="nx">extension</span> <span class="nx">format</span><span class="o" style="font-weight: 600;">.</span> <span class="nx">If</span> <span class="nx">anyone</span> <span class="nx">has</span> <span class="nx">any</span> <span class="nx">recommendation</span> <span class="nx">on</span> <span class="nx">where</span> <span class="nx">to</span> <span class="nx">find</span> <span class="nx">sample</span> <span class="nx">data</span> <span class="nx">in</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">format</span> <span class="nx">it</span> <span class="nx">will</span> <span class="nx">be</span> <span class="nx">much</span> <span class="nx">appreciated</span> <span class="o" style="font-weight: 600;">:</span><span class="p">)</span></span></pre>
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</li>
<li id="57b0c93d13ff3f36774272d1d72501ff621b1ead">
<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#57b0c93d13ff3f36774272d1d72501ff621b1ead"><strong>debian/examples/aluY.chr1.bed</strong></a>
The diff for this file was not included because it is too large.
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<li id="7dabeee48db40e2fd0f6a24e9360ce1d4df01c95">
<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#7dabeee48db40e2fd0f6a24e9360ce1d4df01c95"><strong>debian/examples/gerp.chr1.bed</strong></a>
The diff for this file was not included because it is too large.
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<li id="d081bca44b54ffdaa4b35b86b0f6ec5a3fc02bbf">
<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#d081bca44b54ffdaa4b35b86b0f6ec5a3fc02bbf"><strong>debian/macs-example-data.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;"></span><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">aluY</span><span class="o" style="font-weight: 600;">.</span><span class="nx">chr1</span><span class="o" style="font-weight: 600;">.</span><span class="nx">bed</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">macs</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gerp</span><span class="o" style="font-weight: 600;">.</span><span class="nx">chr1</span><span class="o" style="font-weight: 600;">.</span><span class="nx">bed</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">macs</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">README</span><span class="o" style="font-weight: 600;">.</span><span class="nx">test</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">macs</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">macs</span></span></pre>
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<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#5d623558d4293223717faf2f157094358649fd57"><strong>debian/macs.examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">examples/*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/examples/*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">release/common/*.tree</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></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: navy;">-x</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"macs"</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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>mktemp <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell">cp <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">macs2 callpeak <span class="nt" style="color: navy;">-t</span> aluY.chr1.bed <span class="nt" style="color: navy;">--nomodel</span> <span class="nt" style="color: navy;">-g</span> hs <span class="nt" style="color: navy;">-n</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-B</span> <span class="nt" style="color: navy;">-q</span> 0.01</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">macs2 callpeak <span class="nt" style="color: navy;">-t</span> gerp.chr1.bed <span class="nt" style="color: navy;">--nomodel</span> <span class="nt" style="color: navy;">--broad</span> <span class="nt" style="color: navy;">-g</span> hs <span class="nt" style="color: navy;">--broad-cutoff</span> 0.1</span></pre>
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