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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/dazzdb">Debian Med / dazzdb</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dazzdb/-/commit/e378603afa06d936a929beba73d199d1e635135d">e378603a</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-27T20:29:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install autopkgtests
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/dazzdb/-/commit/3e118a53b97b24457ae2be7d39047ce769ef9e81">3e118a53</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-27T20:29:27+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/dazzdb/-/commit/6bc4f2ef6892bc668b94b09c4c94daf44aba3d41">6bc4f2ef</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-27T20:37:20+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Pranav Ballaney to uploaders
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/dazzdb/-/commit/75865bbd247d88f72555505b657311f48f254e4c">75865bbd</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-07-27T21:40:36+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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debian/README.test
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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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<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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debian/tests/control
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<li class="file-stats">
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/dazzdb/-/compare/23422ea31e9ab92f7ca09299080beccbdd44fad0...75865bbd247d88f72555505b657311f48f254e4c#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <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="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 class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></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">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" 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="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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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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></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/dazzdb/-/compare/23422ea31e9ab92f7ca09299080beccbdd44fad0...75865bbd247d88f72555505b657311f48f254e4c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dazzdb (1.0+git20200115.d8adde7-3) UNRELEASED; urgency=medium</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"> * Install autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add Pranav Ballaney to uploaders</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"> -- Pranav Ballaney <ballaneypranav@gmail.com> Mon, 27 Jul 2020 21:40:08 +0530</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">dazzdb (1.0+git20200115.d8adde7-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Helmut Grohne ]</span>
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<a href="https://salsa.debian.org/med-team/dazzdb/-/compare/23422ea31e9ab92f7ca09299080beccbdd44fad0...75865bbd247d88f72555505b657311f48f254e4c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: dazzdb</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Pranav Ballaney <ballaneypranav@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<a href="https://salsa.debian.org/med-team/dazzdb/-/compare/23422ea31e9ab92f7ca09299080beccbdd44fad0...75865bbd247d88f72555505b657311f48f254e4c#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/dazzdb/-/compare/23422ea31e9ab92f7ca09299080beccbdd44fad0...75865bbd247d88f72555505b657311f48f254e4c#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/dazzdb/-/compare/23422ea31e9ab92f7ca09299080beccbdd44fad0...75865bbd247d88f72555505b657311f48f254e4c#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>dazzdb</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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<pre style="margin: 0;">+<span id="LC7" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</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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15
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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="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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">rangen 1.0 <span class="o" style="font-weight: 600;">></span>R.fasta <span class="c" style="color: #998; font-style: italic;"># Generate a randome 1Mbp sequence R.fasta</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">fasta2DAM R R.fasta <span class="c" style="color: #998; font-style: italic;"># Load it into a .dam DB R.dam</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">dsimulator R <span class="nt" style="color: #000080;">-c20</span><span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">></span>G.fasta <span class="c" style="color: #998; font-style: italic;"># Sample a 20x data sets of the random geneome R</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">fasta2DB G G.fasta <span class="c" style="color: #998; font-style: italic;"># Create a compressed data base of the reads, G.db</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>G.fasta <span class="c" style="color: #998; font-style: italic;"># Redundant, recreate any time with "DB2fasta G"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">DBsplit <span class="nt" style="color: #000080;">-s11</span> G <span class="c" style="color: #998; font-style: italic;"># Split G into 2 parts of size ~ 11MB each</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">DBdust G.1 <span class="c" style="color: #998; font-style: italic;"># Produce a "dust" track on each part</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">DBdust G.2</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">Catrack G dust <span class="c" style="color: #998; font-style: italic;"># Create one track for all of the DB</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> .G.<span class="k" style="font-weight: 600;">*</span>.dust.<span class="k" style="font-weight: 600;">*</span> <span class="c" style="color: #998; font-style: italic;"># Clean up the sub-tracks</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">DBstats <span class="nt" style="color: #000080;">-mdust</span> G <span class="c" style="color: #998; font-style: italic;"># Take a look at the statistics for the database</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span></pre>
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