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<h3>
Andreas Tille 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/61348245f34512f596237648f04566225d6ac870">61348245</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-07-09T17:19:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New binary package featuring example data for testing
</pre>
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<strong><a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/b4df48d4253b6ea79823ad05d055cd81121d5b32">b4df48d4</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-07-09T17:33:09+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>6 changed files:</h4>
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<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
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<li class="file-stats">
<a href="#e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5">
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+
debian/ampliconnoise-examples.install
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<a href="#c21a7da3ce2b89b9f3fe2c0958cc01c8b27bf505">
debian/docs
→
debian/ampliconnoise.docs
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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−
debian/examples
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/30fb5d6056d6425d9f1805ea8c9081d60de194be...b4df48d4253b6ea79823ad05d055cd81121d5b32#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.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">@@ -3,6 +3,7 @@ Notes on how this package can be tested.</td>
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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_line" data-linenumber="4" 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">
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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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<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">sudo</span> <span class="nx">apt</span> <span class="nx">install</span> <span class="nx">ampliconnoise</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span></span>
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<td class="diff-line-num new_line" data-linenumber="7" 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">
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<pre style="margin: 0;"> <span id="LC7" 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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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="9" 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">
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<pre style="margin: 0;"> <span id="LC9" 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="e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/30fb5d6056d6425d9f1805ea8c9081d60de194be...b4df48d4253b6ea79823ad05d055cd81121d5b32#e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5"><strong>debian/ampliconnoise-examples.install</strong></a>
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1
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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>
</pre>
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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="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>
</pre>
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<pre style="margin: 0;">+<span id="LC3" 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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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/30fb5d6056d6425d9f1805ea8c9081d60de194be...b4df48d4253b6ea79823ad05d055cd81121d5b32#c21a7da3ce2b89b9f3fe2c0958cc01c8b27bf505"><strong>debian/docs</strong>
→
<strong>debian/ampliconnoise.docs</strong>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/30fb5d6056d6425d9f1805ea8c9081d60de194be...b4df48d4253b6ea79823ad05d055cd81121d5b32#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ampliconnoise (1.29-9) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ampliconnoise (1.29-9) <span class="idiff left right">unstable</span>; 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Fix edam syntax input+output is singular</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="12" 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">@@ -12,7 +12,6 @@ ampliconnoise (1.29-9) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Add Pranav Ballaney to Uploaders</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> * Update changelog</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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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">@@ -23,6 +22,7 @@ ampliconnoise (1.29-9) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> * New binary package featuring example data for testing</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Thu, 09 Jul 2020 13:17:25 +0530</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/30fb5d6056d6425d9f1805ea8c9081d60de194be...b4df48d4253b6ea79823ad05d055cd81121d5b32#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -32,3 +32,22 @@ Description: removal of noise from 454 sequenced PCR amplicons</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> Previously there was a standalone "Pyronoise" by the same authors and</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> this package includes an updated version. There is also a "Denoiser"</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> in Qiime which is related but distinct.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Package: ampliconnoise-examples</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Enhances: ampliconnoise</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Description: removal of noise from 454 sequenced PCR amplicons (example data)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> AmpliconNoise is a package of applications to clean up high-throughput</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> sequence data. It consists of three main parts:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> Pyronoise - does flowgram-based clustering to spot misreads</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> SeqNoise - removes PCR point mutations</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> Perseus - removes PCR chimeras without the need for a set of reference</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> sequences</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> Previously there was a standalone "Pyronoise" by the same authors and</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> this package includes an updated version. There is also a "Denoiser"</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> in Qiime which is related but distinct.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> This package contains example data for ampliconnoise.</span></pre>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/30fb5d6056d6425d9f1805ea8c9081d60de194be...b4df48d4253b6ea79823ad05d055cd81121d5b32#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests/ref</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/tests/Run.sh</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Test/C005.dat</span></pre>
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