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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:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dazzdb/-/commit/2bbb7e66a85b88d8e91a89b9a0b3203c13c02acb">2bbb7e66</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-07-27T22:41:14+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run autopkgtests with seeds to compare output with checksums
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<h4>1 changed file:</h4>
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/dazzdb/-/commit/2bbb7e66a85b88d8e91a89b9a0b3203c13c02acb#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -14,15 +14,47 @@ fi</td>
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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="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="LC16" class="line" lang="shell"></span>
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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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<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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<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="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generate a random 1Mbp sequence R.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">rangen 1.0 <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span> R.fasta</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"e259b3524f74d97e70ecf97f9078b77e R.fasta"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Load it into a .dam DB R.dam</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">fasta2DAM R R.fasta</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"ab5f001069bd928051b01c42bbf91f5b .R.bps"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"89ad93fbaa6e7a645c76ffdf1fb43792 .R.hdr"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"8ebbdc9428ac6f3b5e407ee43a86ecc4 .R.idx"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"c4795a84d7a81407c9a25b75c4a96621 R.dam"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><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="LC29" class="line" lang="shell">dsimulator R <span class="nt" style="color: #000080;">-c20</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span> G.fasta</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"4382a3340b21340efcc5c878c1e07216 G.fasta"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><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="LC33" class="line" lang="shell">fasta2DB G G.fasta</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"fa422bad76a2b9119c182be811f389d1 .G.bps"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><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="LC38" class="line" lang="shell">DBsplit <span class="nt" style="color: #000080;">-s11</span> G</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"25a447c3375b8581314e7c92641b01a2 .G.idx"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"f6cec403e88918a5c93f265de226ca75 G.db"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><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="LC43" class="line" lang="shell">DBdust G.1</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"4d128adb1b639552ea751f6e1b4d35bb .G.1.dust.anno"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"e8dcdd4094198898e51ac431cd3b071b .G.1.dust.data"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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24
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell">DBdust G.2</span>
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25
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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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<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="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"3957f13eabc099461179b1b5be3393be .G.2.dust.anno"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"7ae21880213ececd5411097bc5787386 .G.2.dust.data"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Create one track for all of the DB</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell">Catrack G dust</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"99cd6dcb6c6206f4770500ec7e6c0bc3 .G.dust.anno"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"df77d8ad1ca51e730bb11597d2c8bd93 .G.dust.data"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Take a look at the statistics for the database</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell">DBstats <span class="nt" style="color: #000080;">-mdust</span> G <span class="o" style="font-weight: 600;">></span> result</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"5c5c5f89a9ae055cc06487febc6adb3d result"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span>
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28
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"></span></pre>
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