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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/ampliconnoise">Debian Med / ampliconnoise</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/83bf76b9337419b4e1cc3d053fecff08d755964e">83bf76b9</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-24T05:15:34+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace reference files with their checksums
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5">
debian/ampliconnoise-examples.install
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<a href="#c2c4775f6393a3870aaa44321d5d2987b5cc093a">
<span class="deleted-file">
−
debian/tests/ref/C005.tar.xz
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/83bf76b9337419b4e1cc3d053fecff08d755964e#e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5"><strong>debian/ampliconnoise-examples.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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">ref</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">ampliconnoise</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="LC1" 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">sh</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">ampliconnoise</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">Test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">C005</span><span class="o" style="font-weight: 600;">.</span><span class="nx">dat</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">ampliconnoise</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<li id="c2c4775f6393a3870aaa44321d5d2987b5cc093a">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/83bf76b9337419b4e1cc3d053fecff08d755964e#c2c4775f6393a3870aaa44321d5d2987b5cc093a"><strong>debian/tests/ref/C005.tar.xz</strong>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/83bf76b9337419b4e1cc3d053fecff08d755964e#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,19 +14,23 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-R</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">./Run.sh C005.dat</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> C005_s60_c01 C005_s60_c01_T220_s30_c08</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>ref <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">tar </span>xvf C005.tar.xz</span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>C005.tar.xz</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># pwd</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">./Run.sh C005.dat</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>file <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"../</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"> diff <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"../</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> is identical to its reference."</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Output precomputed checksums to file</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>d6887d8e940f823d6e1070692d438d2d C005_X.list <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>d20be5a6fce78395d767e84ed9e78ad8 C005_s60_c01.mapping <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>3333dd1c1c9315b1bc0ea53eb5e408c2 C005_s60_c01.master <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>14371657c17ea44b1bffd3779ac4d50b C005_s60_c01_T220.fa <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" 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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>ab7114c307e8faddf0e3e6da1c26081d C005_s60_c01_T220_S.list <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>7c0dd9d92aaeb2c0dd32369ea066afff C005_s60_c01_T220_s30_c08.mapping <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>4ce84f19c80d64f800602cf6c145bdf2 C005_s60_c01_T220_s30_c08_P.fa <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>97467bf7a102958a51b11a26fa17f7f2 C005_s60_c01_T220_s30_c08_P.list <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>d73458b99089769c9363f6584c085524 C005_s60_c01_T220_s30_c08_P.otu <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>bd85775030379914ce5c8d90b89941e7 C005_s60_c01_T220_s30_c08_P.tree <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>4ce84f19c80d64f800602cf6c145bdf2 C005_s60_c01_T220_s30_c08_cd.fa <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>4215fa70dfd3e4b51368fbbe40ca7021 C005_s60_c01_T220_s30_c08_cd.mapping <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>b7e06a3f231925c35ee3b747bbe5ae31 C005_s60_c01_cd.fa <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>d0fc9be11a1817fcf5afdad0a1a560b7 C005_s60_c01_cd.qual <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span></pre>
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