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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pbgenomicconsensus">Debian Med / pbgenomicconsensus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258">a0579e22</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T15:36:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.3</pre>
</li>
</ul>
<h4>27 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#99c738e7d1f1f228db3f2802b37507b0ff0d0c0d">
GenomicConsensus/ResultCollector.py
</a>
</li>
<li class="file-stats">
<a href="#438f7a424514a3e27a4a6fd3606f44eb75491140">
GenomicConsensus/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#e98081513decc5c2f9c0b043551255f723e3e716">
GenomicConsensus/arrow/arrow.py
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<li class="file-stats">
<a href="#48d5db9c8417ce95dae83f2d5437fea893c40f2a">
GenomicConsensus/arrow/model.py
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<li class="file-stats">
<a href="#008d0e3444457abc4db366abc89cfc552c420f08">
GenomicConsensus/io/VariantsGffWriter.py
</a>
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<li class="file-stats">
<a href="#07e6c57b2dbb1ad4d9cbe7d61e28b7da0035184e">
GenomicConsensus/io/VariantsVcfWriter.py
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</li>
<li class="file-stats">
<a href="#4e9778bec0a993507bd561e9780cca7aea66c050">
GenomicConsensus/options.py
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<li class="file-stats">
<a href="#15717a3bfe329895159f1f07cab42c961286f088">
GenomicConsensus/poa/poa.py
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<li class="file-stats">
<a href="#4b0c4cfefba6ba2c26cd101d3e75167978675c95">
GenomicConsensus/quiver/quiver.py
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<li class="file-stats">
<a href="#e6b22af8a7794963f75a0e874a49e6d946562e46">
GenomicConsensus/variants.py
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<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSES
→
LICENSE
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<li class="file-stats">
<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">
MANIFEST.in
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9">
bamboo_build.sh
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<li class="file-stats">
<a href="#4ba2d7a35ab8ebb7591ec82843466797567f7a10">
bin/gffToBed
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<li class="file-stats">
<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">
doc/conf.py
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<li class="file-stats">
<a href="#9368445e6ae7ddf3770c5b9346191b8c3783f653">
scripts/ci/build.sh
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<li class="file-stats">
<a href="#9ea7ba3e397712057afe008b4efa78e61af3d9cd">
<span class="new-file">
+
scripts/ci/setup.sh
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<li class="file-stats">
<a href="#dc4d5d1220b0cd2b76cb436a076ddf99d8de0fdb">
<span class="new-file">
+
scripts/ci/test.sh
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<li class="file-stats">
<a href="#17578dc0813a46c3b563d8bbc40c5360e1124b3e">
<span class="deleted-file">
−
scripts/nightly/build.sh
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<li class="file-stats">
<a href="#3dba9412adb7094797d775feafcd655f24bb726c">
<span class="deleted-file">
−
scripts/nightly/test.sh
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#80753364ed500dbeacc378880ea8eacc86b0ccc3">
tests/cram/arrow-all4mer-diploid.t
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<li class="file-stats">
<a href="#fc0f82229e23cec09bfca2c1e4dfde6124135457">
tests/cram/internal/quiver-ecoli.t
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<li class="file-stats">
<a href="#92b57ec44fc684442554c3d517b59da4ec8964b2">
tests/cram/quiver-noqvs-test.t
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<li class="file-stats">
<a href="#f37b7319b5fc970aa5502c7a9001ef404e6ec91d">
tests/cram/version.t
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</li>
<li class="file-stats">
<a href="#ba6ee8ca3889715aebcca9ac8140282add1ca6ed">
tests/unit/test_summarize_consensus.py
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</li>
</ul>
<h4>Changes:</h4>
<li id="99c738e7d1f1f228db3f2802b37507b0ff0d0c0d">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#99c738e7d1f1f228db3f2802b37507b0ff0d0c0d"><strong>GenomicConsensus/ResultCollector.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" 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">@@ -22,16 +22,22 @@ class ResultCollector(object):</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" 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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<td class="diff-line-num new_line" data-linenumber="23" 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="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num old_line" data-linenumber="24" 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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<td class="diff-line-num new_line" data-linenumber="24" 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="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">onStart</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="26" 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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<td class="diff-line-num new_line old" data-linenumber="25" 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="LC26" class="line" lang="python"> <span class="n" style="color: #333;">sentinelsReceived</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" 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="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">sentinelsReceived</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">numWorkers</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="28" 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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_resultsQueue</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="29" 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="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="30" 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="LC30" class="line" lang="python"> <span class="n" style="color: #333;">sentinelsReceived</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="32" 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="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">onResult</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="33" 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="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">onFinish</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">sentinelsReceived</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">sentinelsReceived</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">numWorkers</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_resultsQueue</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">sentinelsReceived</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">onResult</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Even on error, we want the files to be closed.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Otherwise, e.g., we could end up with empty .gz files,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># which are invalid.</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># And for debugging, we should see the current state of output.</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This will run even on KeyboardInterrupt.</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">onFinish</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Analysis completed."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">doProfiling</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" 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>
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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">@@ -80,7 +86,6 @@ class ResultCollector(object):</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_flushContigIfCompleted</span><span class="p">(</span><span class="n" style="color: #333;">window</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">onFinish</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Analysis completed."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastaWriter</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastaWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastqWriter</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastqWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gffWriter</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#438f7a424514a3e27a4a6fd3606f44eb75491140"><strong>GenomicConsensus/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Author: David Alexander, David Seifert</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">print_function</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__VERSION__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.3.<span class="idiff left right">2</span>'</span> <span class="c1" style="color: #998; font-style: italic;"># don't forget to update setup.py and doc/conf.py too</span></span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__VERSION__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.3.<span class="idiff left right">3</span>'</span> <span class="c1" style="color: #998; font-style: italic;"># don't forget to update setup.py and doc/conf.py too</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#e98081513decc5c2f9c0b043551255f723e3e716"><strong>GenomicConsensus/arrow/arrow.py</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">@@ -11,7 +11,7 @@ from ..ResultCollector import ResultCollectorProcess, ResultCollectorThread</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.consensus</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Consensus</span><span class="p">,</span> <span class="n" style="color: #333;">ArrowConsensus</span><span class="p">,</span> <span class="n" style="color: #333;">join</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.windows</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">kSpannedIntervals</span><span class="p">,</span> <span class="n" style="color: #333;">holes</span><span class="p">,</span> <span class="n" style="color: #333;">subWindow</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.variants</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">filterVariants</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">annotateVariants</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.variants</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">annotateVariants</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.arrow</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">diploid</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">die</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></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">@@ -99,14 +99,11 @@ def consensusAndVariantsForWindow(alnFile, refWindow, referenceContig,</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">ai</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">diploid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">arrowConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">polishDiploid</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">filteredVars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filterVariants</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minCoverage</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minConfidence</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">variants_</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Annotate?</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotateGFF</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">filteredVars</span></span><span class="p">,</span> <span class="n" style="color: #333;">clippedAlns</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">variants_</span></span><span class="p">,</span> <span class="n" style="color: #333;">clippedAlns</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">variants</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">filteredVars</span></span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">variants</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">variants_</span></span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The nascent consensus sequence might contain ambiguous bases, these</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># need to be removed as software in the wild cannot deal with such</span></span>
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<li id="48d5db9c8417ce95dae83f2d5437fea893c40f2a">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#48d5db9c8417ce95dae83f2d5437fea893c40f2a"><strong>GenomicConsensus/arrow/model.py</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">@@ -34,7 +34,7 @@ class ArrowConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">computeConfidence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">readStumpinessThreshold</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">minReadScore</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.75</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">minHqRegionSnr</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;"><span class="idiff left right">3.7</span>5</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">minHqRegionSnr</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;"><span class="idiff left right">2.</span>5</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">minZScore</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">3.5</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">minAccuracy</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.82</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">maskRadius</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#008d0e3444457abc4db366abc89cfc552c420f08"><strong>GenomicConsensus/io/VariantsGffWriter.py</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">@@ -47,6 +47,9 @@ class VariantsGffWriter(object):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">,</span> <span class="n" style="color: #333;">referenceEntries</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GffWriter</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">[</span><span class="s" style="color: #d14;">"minConfidence"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">[</span><span class="s" style="color: #d14;">"minCoverage"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writeHeader</span><span class="p">(</span><span class="s" style="color: #d14;">"##pacbio-variant-version 2.1"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writeHeader</span><span class="p">(</span><span class="s" style="color: #d14;">"##date </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ctime</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writeHeader</span><span class="p">(</span><span class="s" style="color: #d14;">"##feature-ontology </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ONTOLOGY_URL</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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="64" 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">@@ -61,7 +64,8 @@ class VariantsGffWriter(object):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeVariants</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">variants</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">var</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">variants</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writeRecord</span><span class="p">(</span><span class="n" style="color: #333;">toGffRecord</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">>=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">confidence</span> <span class="o" style="font-weight: 600;">>=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writeRecord</span><span class="p">(</span><span class="n" style="color: #333;">toGffRecord</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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67
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_gffWriter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span></pre>
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<li id="07e6c57b2dbb1ad4d9cbe7d61e28b7da0035184e">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#07e6c57b2dbb1ad4d9cbe7d61e28b7da0035184e"><strong>GenomicConsensus/io/VariantsVcfWriter.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" 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">@@ -21,8 +21,11 @@ class VariantsVcfWriter(object):</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">,</span> <span class="n" style="color: #333;">referenceEntries</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">[</span><span class="s" style="color: #d14;">"minConfidence"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">[</span><span class="s" style="color: #d14;">"minCoverage"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> ##fileformat=VCFv4.<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> ##fileformat=VCFv4.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> ##fileDate={date}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> ##source=GenomicConsensusV{version}</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> ##reference={reference}'''</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></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">@@ -37,6 +40,26 @@ class VariantsVcfWriter(object):</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">entry</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO(lhepler): evaluate adding md5 hexdigest here on large genomes</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">optionsDict</span><span class="p">[</span><span class="s" style="color: #d14;">"diploid"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># filters</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidenceFilterID</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'q{}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'##FILTER=<ID={id},Description="Quality below {confidence}">'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidenceFilterID</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">confidence</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverageFilterID</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'c{}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'##FILTER=<ID={id},Description="Coverage below {coverage}">'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverageFilterID</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#CHROM</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">POS</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">REF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ALT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QUAL</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILTER</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">INFO"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeVariants</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">variants</span><span class="p">):</span></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">@@ -79,6 +102,15 @@ class VariantsVcfWriter(object):</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DP={0}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coverage</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">freq</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">";"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">freq</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># failed filters</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">failedFilters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">confidence</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">failedFilters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minConfidenceFilterID</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverage</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">failedFilters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minCoverageFilterID</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">filterText</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">";"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">failedFilters</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">failedFilters</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"{chrom}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{pos}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{id}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{ref}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{alt}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{qual}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{filter}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{info}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reference</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">idToFullName</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">refId</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pos</span><span class="p">,</span></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">@@ -86,7 +118,7 @@ class VariantsVcfWriter(object):</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ref</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">alt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">alt</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">confidence</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">"PASS"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left right">filterText</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">info</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_vcfFile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#4e9778bec0a993507bd561e9780cca7aea66c050"><strong>GenomicConsensus/options.py</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">@@ -59,7 +59,7 @@ class Constants(object):</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MAX_COVERAGE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MIN_MAPQV</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MIN_READSCORE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.65</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MIN_HQREGIONSNR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;"><span class="idiff left right">3.7</span>5</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MIN_HQREGIONSNR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;"><span class="idiff left right">2.</span>5</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MIN_ZSCORE</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">3.5</span></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MIN_ACCURACY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.82</span></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_MASK_RADIUS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#15717a3bfe329895159f1f07cab42c961286f088"><strong>GenomicConsensus/poa/poa.py</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">@@ -11,7 +11,7 @@ from .. import reference</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..options</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">options</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..consensus</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Consensus</span><span class="p">,</span> <span class="n" style="color: #333;">join</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..windows</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">kSpannedIntervals</span><span class="p">,</span> <span class="n" style="color: #333;">holes</span><span class="p">,</span> <span class="n" style="color: #333;">subWindow</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..variants</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">filterVariants</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">annotateVariants</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..variants</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;">annotateVariants</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..Worker</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">WorkerProcess</span><span class="p">,</span> <span class="n" style="color: #333;">WorkerThread</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..ResultCollector</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ResultCollectorProcess</span><span class="p">,</span> <span class="n" style="color: #333;">ResultCollectorThread</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..arrow.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">variantsFromAlignment</span></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">@@ -32,7 +32,7 @@ class PoaConfig(object):</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">noEvidenceConsensus</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"nocall"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">readStumpinessThreshold</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">minReadScore</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.75</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">minHqRegionSnr</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;"><span class="idiff left right">3.7</span>5</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">minHqRegionSnr</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;"><span class="idiff left right">2.</span>5</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minMapQV</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minMapQV</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minPoaCoverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minPoaCoverage</span></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">@@ -191,14 +191,11 @@ def poaConsensusAndVariants(alnFile, refWindow, referenceContig,</td>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">consensusAndVariantsForAlignments</span><span class="p">(</span><span class="n" style="color: #333;">subWin</span><span class="p">,</span> <span class="n" style="color: #333;">intRefSeq</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">clippedAlns</span><span class="p">,</span> <span class="n" style="color: #333;">poaConfig</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">filteredVars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filterVariants</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minCoverage</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minConfidence</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">variants_</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Annotate?</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotateGFF</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">filteredVars</span></span><span class="p">,</span> <span class="n" style="color: #333;">clippedAlns</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">variants_</span></span><span class="p">,</span> <span class="n" style="color: #333;">clippedAlns</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">variants</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">filteredVars</span></span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">variants</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">variants_</span></span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">css</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Consensus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">noCallConsensus</span><span class="p">(</span><span class="n" style="color: #333;">poaConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">noEvidenceConsensus</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">subWin</span><span class="p">,</span> <span class="n" style="color: #333;">intRefSeq</span><span class="p">)</span></span>
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<li id="4b0c4cfefba6ba2c26cd101d3e75167978675c95">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#4b0c4cfefba6ba2c26cd101d3e75167978675c95"><strong>GenomicConsensus/quiver/quiver.py</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">@@ -11,7 +11,7 @@ from ..ResultCollector import ResultCollectorProcess, ResultCollectorThread</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.consensus</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Consensus</span><span class="p">,</span> <span class="n" style="color: #333;">QuiverConsensus</span><span class="p">,</span> <span class="n" style="color: #333;">join</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.windows</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">kSpannedIntervals</span><span class="p">,</span> <span class="n" style="color: #333;">holes</span><span class="p">,</span> <span class="n" style="color: #333;">subWindow</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.variants</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">filterVariants</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">annotateVariants</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.variants</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">annotateVariants</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">GenomicConsensus.quiver</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">diploid</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">GenomicConsensus.quiver.model</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">M</span></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">@@ -99,14 +99,11 @@ def consensusAndVariantsForWindow(cmpH5, refWindow, referenceContig,</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">mms</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">filteredVars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filterVariants</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minCoverage</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minConfidence</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">variants_</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Annotate?</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotateGFF</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">filteredVars</span></span><span class="p">,</span> <span class="n" style="color: #333;">clippedAlns</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">variants_</span></span><span class="p">,</span> <span class="n" style="color: #333;">clippedAlns</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">variants</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">filteredVars</span></span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">variants</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left right">variants_</span></span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">css</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QuiverConsensus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">noCallConsensus</span><span class="p">(</span><span class="n" style="color: #333;">quiverConfig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">noEvidenceConsensus</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">subWin</span><span class="p">,</span> <span class="n" style="color: #333;">intRefSeq</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#e6b22af8a7794963f75a0e874a49e6d946562e46"><strong>GenomicConsensus/variants.py</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">@@ -88,11 +88,6 @@ class Variant(CommonEqualityMixin):</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotations</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filterVariants</span><span class="p">(</span><span class="n" style="color: #333;">minCoverage</span><span class="p">,</span> <span class="n" style="color: #333;">minConfidence</span><span class="p">,</span> <span class="n" style="color: #333;">variants</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span> <span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">variants</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minCoverage</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">confidence</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minConfidence</span><span class="p">))</span> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotateVariants</span><span class="p">(</span><span class="n" style="color: #333;">variants</span><span class="p">,</span> <span class="n" style="color: #333;">alns</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Operates in place</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">variants</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">include LICENSE<span class="idiff left right">S</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">include LICENSE</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"># Quiver model definitions</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">graft GenomicConsensus/quiver/resources</span></pre>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;">GenomicConsensus (quiver, arrow) [](https://circleci.com/gh/PacificBiosciences/GenomicConsensus)</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">align=</span><span class="s" style="color: #d14;">"center"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"http://www.pacb.com/wp-content/themes/pacific-biosciences/img/pacific-biosciences-logo-mobile.svg"</span><span class="nt" style="color: #000080;">/></h1></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">align=</span><span class="s" style="color: #d14;">"center"</span><span class="nt" style="color: #000080;">></span>GenomicConsensus<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">align=</span><span class="s" style="color: #d14;">"center"</span><span class="nt" style="color: #000080;">></span>Genome polishing and variant calling.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">***</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">The <span class="sb" style="color: #d14;">``GenomicConsensus``</span> package provides the <span class="sb" style="color: #d14;">``variantCaller``</span> tool,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown">which allows you to apply the Quiver or Arrow algorithm to mapped</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">PacBio reads to get consensus and variant calls.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="gh" style="color: #999;">Background on Quiver and Arrow</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Availability</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">Latest version can be installed via bioconda package <span class="sb" style="color: #d14;">`genomicconsensus`</span>.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">Please refer to our <span class="p">[</span><span class="nv" style="color: #008080;">official pbbioconda page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/PacificBiosciences/pbbioconda</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">for information on Installation, Support, License, Copyright, and Disclaimer.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Background on Quiver and Arrow</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Quiver*</span> is the legacy consensus model based on a conditional random</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">field approach. Quiver enables consensus accuracies on genome</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">@@ -24,13 +32,7 @@ Quiver is supported for PacBio RS data. Arrow is supported for PacBio</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown">Sequel data and RS data with the P6-C4 chemistry.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="gh" style="color: #999;">Getting GenomicConsensus</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">Casual users should get <span class="sb" style="color: #d14;">``GenomicConsensus``</span> from the</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">SMRTanalysis software bundle</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.pacb.com/support/software-downloads/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="gh" style="color: #999;">Running</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="gh" style="color: #999;">## Running</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gh" style="color: #999;">-------</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown">Basic usage is as follows:</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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="58" 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">@@ -56,8 +58,7 @@ FASTQ file.</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"> release of SMRTanalysis 3.0 or build from GitHub sources.<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"><span class="gh" style="color: #999;">More documentation</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## More documentation</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">More detailed installation and running instructions</span><span class="p">](</span><span class="sx" style="color: #d14;">./doc/HowTo.rst</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">FAQ</span><span class="p">](</span><span class="sx" style="color: #d14;">./doc/FAQ.rst</span><span class="p">)</span></span>
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<li id="8ab4e94f59343a8b2d003b0b47d21fff1724bfd9">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9"><strong>bamboo_build.sh</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;">#!/<span class="idiff left right">bin/</span>bash</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/bin/env </span>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;">-vex</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">bash <span class="nt" style="color: #000080;">-vex</span> scripts/ci/build.sh <span class="nv" style="color: #008080;">$@</span></span></pre>
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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="c" style="color: #998; font-style: italic;">################</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># DEPENDENCIES #</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################</span></span>
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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="c" style="color: #998; font-style: italic;">## Load modules</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">type </span>module <span class="o" style="font-weight: 600;">></span>& /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">module purge</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># python deps</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">module load python/2</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">module load cram</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">module load swig</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="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># One fairly fast cram-test,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># quiver-tinyLambda-coverage-islands.t,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># was moved from cram/internal. It needs some GNU modules.</span></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;"># If that becomes a problem, just move it back to cram/internal.</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">module load mummer</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">module load blasr/2.3.0</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">module load exonerate/2.0.0</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">module load gfftools/dalexander</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">bamboo_planRepository_branchName</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>master<span class="p">)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> module load ConsensusCore/master</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> module load unanimity/master</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="p">;;</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;">*</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> module load ConsensusCore/develop</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> module load unanimity/develop</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="p">;;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Use PYTHONUSERBASE in lieu of virtualenv</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PYTHONUSERBASE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PWD</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/build"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PYTHONUSERBASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/bin:</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PATH</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source </span>scripts/ci/setup.sh</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source </span>scripts/ci/build.sh</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source </span>scripts/ci/test.sh</span></pre>
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<br>
</li>
<li id="4ba2d7a35ab8ebb7591ec82843466797567f7a10">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#4ba2d7a35ab8ebb7591ec82843466797567f7a10"><strong>bin/gffToBed</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="57" 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">@@ -57,7 +57,20 @@ class CoverageBedRecord(BedRecord):</td>
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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chromStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chromEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span></span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'meanCov'</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">gff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cov2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 'coverage' field output by variantCaller nowadays</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">gff</span><span class="p">,</span> <span class="s" style="color: #d14;">'coverage'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># backwards compatible field from quiver days</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">gff</span><span class="p">,</span> <span class="s" style="color: #d14;">'cov2'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Could not determine coverage from input GFF'</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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61
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">bed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span></span>
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62
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bed</span></span>
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63
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></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">@@ -16,7 +16,7 @@ from __future__ import absolute_import, division, print_function</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">os</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dirname</span><span class="p">,</span> <span class="n" style="color: #333;">join</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">__VERSION__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.3.<span class="idiff left right">2</span>'</span> <span class="c1" style="color: #998; font-style: italic;"># don't forget to update setup.py and GenomicConsensus/__init__.py too</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">__VERSION__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.3.<span class="idiff left right">3</span>'</span> <span class="c1" style="color: #998; font-style: italic;"># don't forget to update setup.py and GenomicConsensus/__init__.py too</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If extensions (or modules to document with autodoc) are in another directory,</span></span>
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<li id="9368445e6ae7ddf3770c5b9346191b8c3783f653">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#9368445e6ae7ddf3770c5b9346191b8c3783f653"><strong>scripts/ci/build.sh</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;">#!/<span class="idiff left right">bin/</span>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: #000080;">-<span class="idiff left">euo</span></span><span class="idiff right"> pipefail</span></span>
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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;">#!/<span class="idiff left right">usr/bin/env </span>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: #000080;">-<span class="idiff left right">vex</span></span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# DEPENDENCIES"</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Load modules"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">type </span>module <span class="o" style="font-weight: 600;">></span>& /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell">module load git</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell">module load gcc</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell">module load cmake ninja</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell">module load cram</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell">module load swig ccache boost</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">CXX</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CXX</span><span class="s2" style="color: #d14;"> -static-libstdc++"</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">GXX</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CXX</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span>CXX GXX</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$USER</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"bamboo"</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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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CCACHE_DIR</span><span class="o" style="font-weight: 600;">=</span>/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CCACHE_TEMPDIR</span><span class="o" style="font-weight: 600;">=</span>/scratch/bamboo.ccache_tempdir</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CCACHE_COMPILERCHECK</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'%compiler% -dumpversion'</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CCACHE_BASEDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#########</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># BUILD #</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#########</span></span>
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21
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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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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Use PYTHONUSERBASE in lieu of virtualenv"</span></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">
23
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<td class="diff-line-num new_line old" data-linenumber="8" 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;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/build/bin:/mnt/software/a/anaconda2/4.2.0/bin:<span class="nv" style="color: #008080;">$PATH</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PYTHONUSERBASE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/build</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># pip 9 create some problem with egg style install so don't upgrade pip</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nv" style="color: #008080;">PIP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"pip --cache-dir=</span><span class="nv" style="color: #008080;">$PWD</span><span class="s2" style="color: #d14;">/.pip --disable-pip-version-check"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># install</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/mnt/software/p/python/wheelhouse/develop/"</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--find-links</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-e</span> <span class="nb" style="color: #0086b3;">.</span></span>
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27
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Install pip modules"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="29" 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">
29
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">NX3PBASEURL</span><span class="o" style="font-weight: 600;">=</span>http://nexus/repository/unsupported/pitchfork/gcc-6.4.0</span>
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30
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC30" class="line" lang="shell"><span class="nv" style="color: #008080;">NXSABASEURL</span><span class="o" style="font-weight: 600;">=</span>http://nexus/repository/maven-snapshots/pacbio/sat</span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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="LC31" class="line" lang="shell"><span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="se" style="color: #d14;">\</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"> <span class="nv" style="color: #008080;">$NX3PBASEURL</span>/pythonpkgs/pysam-0.13-cp27-cp27mu-linux_x86_64.whl <span class="se" style="color: #d14;">\</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"> <span class="nv" style="color: #008080;">$NX3PBASEURL</span>/pythonpkgs/xmlbuilder-1.0-cp27-none-any.whl <span class="se" style="color: #d14;">\</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"> <span class="nv" style="color: #008080;">$NX3PBASEURL</span>/pythonpkgs/avro-1.7.7-cp27-none-any.whl <span class="se" style="color: #d14;">\</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"> iso8601 <span class="se" style="color: #d14;">\</span></span>
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36
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC36" class="line" lang="shell"> <span class="nv" style="color: #008080;">$NX3PBASEURL</span>/pythonpkgs/tabulate-0.7.5-cp27-none-any.whl <span class="se" style="color: #d14;">\</span></span>
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37
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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> coverage</span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-sfn</span> ../data _deps/pacbiotestdata/pbtestdata/data</span>
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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"><span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">-e</span> _deps/pacbiotestdata</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">-e</span> _deps/pbcore</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">-e</span> _deps/pbcommand</span>
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<td class="diff-line-num old old_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Get external dependencies"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-s</span> <span class="nt" style="color: #000080;">-L</span> <span class="nv" style="color: #008080;">$NX3PBASEURL</span>/zlib-1.2.8.tgz | <span class="nb" style="color: #0086b3;">tar </span>zxf - <span class="nt" style="color: #000080;">-C</span> build</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-s</span> <span class="nt" style="color: #000080;">-L</span> <span class="nv" style="color: #008080;">$NXSABASEURL</span>/htslib/htslib-1.1-SNAPSHOT.tgz | <span class="nb" style="color: #0086b3;">tar </span>zxf - <span class="nt" style="color: #000080;">-C</span> build</span>
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<td class="diff-line-num old old_line" data-linenumber="46" 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">
46
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC46" class="line" lang="shell"></span>
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47
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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;">"## Fetch unanimity </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">submodules</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd </span>_deps/unanimity <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> git checkout <span class="nb" style="color: #0086b3;">.</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> git clean <span class="nt" style="color: #000080;">-xdf</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> third-party/pbbam third-party/pbcopper <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-sfn</span> <span class="nv" style="color: #008080;">$PWD</span>/../pbbam third-party/pbbam <span class="se" style="color: #d14;">\</span></span>
</pre>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-sfn</span> <span class="nv" style="color: #008080;">$PWD</span>/../pbcopper third-party/pbcopper <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the reason to use $PWD/.. full path is that pip will copy it to /tmp</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# BUILD"</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## install ConsensusCore"</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd </span>_deps/ConsensusCore <span class="se" style="color: #d14;">\</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> python setup.py bdist_wheel <span class="nt" style="color: #000080;">--boost</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BOOST_ROOT</span> <span class="se" style="color: #d14;">\</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo </span>dist/ConsensusCore-<span class="k" style="font-weight: 600;">*</span>.whl | <span class="se" style="color: #d14;">\</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"> xargs <span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--verbose</span> <span class="o" style="font-weight: 600;">)</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell"></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## pip install CC2"</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd </span>_deps/unanimity <span class="se" style="color: #d14;">\</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">CMAKE_BUILD_TYPE</span><span class="o" style="font-weight: 600;">=</span>ReleaseWithAssert <span class="se" style="color: #d14;">\</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="shell"> <span class="nv" style="color: #008080;">CMAKE_COMMAND</span><span class="o" style="font-weight: 600;">=</span>cmake <span class="se" style="color: #d14;">\</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"> <span class="nv" style="color: #008080;">ZLIB_INCLUDE_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/../../build/include <span class="se" style="color: #d14;">\</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="shell"> <span class="nv" style="color: #008080;">ZLIB_LIBRARY</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/../../build/lib/libz.so <span class="se" style="color: #d14;">\</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell"> <span class="nv" style="color: #008080;">VERBOSE</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">$PIP</span> wheel <span class="nt" style="color: #000080;">--verbose</span> <span class="nb" style="color: #0086b3;">.</span> <span class="se" style="color: #d14;">\</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--verbose</span> ConsensusCore2-<span class="k" style="font-weight: 600;">*</span>.whl <span class="o" style="font-weight: 600;">)</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## install GC"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># produce wheel</span></span>
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73
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell">python setup.py bdist_wheel</span></pre>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="shell"><span class="nv" style="color: #008080;">$PIP</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--verbose</span> dist/GenomicConsensus-<span class="k" style="font-weight: 600;">*</span>.whl</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# TEST"</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## CC2 version test"</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="shell">python <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"import ConsensusCore2 ; print ConsensusCore2.__version__"</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="shell"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## test CC2 via GC"</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell">coverage run <span class="nt" style="color: #000080;">--source</span> GenomicConsensus <span class="nt" style="color: #000080;">-m</span> py.test <span class="nt" style="color: #000080;">--verbose</span> <span class="nt" style="color: #000080;">--junit-xml</span><span class="o" style="font-weight: 600;">=</span>nosetests.xml tests/unit</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="shell"></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># One fairly fast cram-test,</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># quiver-tinyLambda-coverage-islands.t,</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># was moved from cram/internal. It needs some GNU modules.</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If that becomes a problem, just move it back to cram/internal.</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="shell">module load mummer</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell">module load exonerate/2.0.0</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="shell"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run fairly fast cram tests.</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell">make basic-tests</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="shell"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="shell">coverage xml <span class="nt" style="color: #000080;">-o</span> coverage.xml</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s@filename="@filename="./@g'</span> coverage.xml</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="shell"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="shell"><span class="nv" style="color: #008080;">ConsensusCore_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nv" style="color: #008080;">$PIP</span> freeze|grep <span class="s1" style="color: #d14;">'ConsensusCore=='</span>|awk <span class="nt" style="color: #000080;">-F</span> <span class="s1" style="color: #d14;">'=='</span> <span class="s1" style="color: #d14;">'{print $2}'</span><span class="sb" style="color: #d14;">`</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="shell"><span class="nv" style="color: #008080;">ConsensusCore2_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nv" style="color: #008080;">$PIP</span> freeze|grep <span class="s1" style="color: #d14;">'ConsensusCore2=='</span>|awk <span class="nt" style="color: #000080;">-F</span> <span class="s1" style="color: #d14;">'=='</span> <span class="s1" style="color: #d14;">'{print $2}'</span><span class="sb" style="color: #d14;">`</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="shell"><span class="nv" style="color: #008080;">GenomicConsensus_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nv" style="color: #008080;">$PIP</span> freeze|grep <span class="s1" style="color: #d14;">'GenomicConsensus=='</span>|awk <span class="nt" style="color: #000080;">-F</span> <span class="s1" style="color: #d14;">'=='</span> <span class="s1" style="color: #d14;">'{print $2}'</span><span class="sb" style="color: #d14;">`</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"_</span><span class="nv" style="color: #008080;">$bamboo_planRepository_1_branch</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"_develop"</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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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">NEXUS_BASEURL</span><span class="o" style="font-weight: 600;">=</span>http://ossnexus.pacificbiosciences.com/repository</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="shell"> <span class="nv" style="color: #008080;">NEXUS_URL</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$NEXUS_BASEURL</span>/unsupported/gcc-6.4.0</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="shell"> curl <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">--upload-file</span> _deps/ConsensusCore/dist/ConsensusCore-<span class="k" style="font-weight: 600;">*</span>.whl <span class="nv" style="color: #008080;">$NEXUS_URL</span>/pythonpkgs/ConsensusCore-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ConsensusCore_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-cp27-cp27mu-linux_x86_64</span>.whl</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell"> curl <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">--upload-file</span> _deps/unanimity/ConsensusCore2-<span class="k" style="font-weight: 600;">*</span>.whl <span class="nv" style="color: #008080;">$NEXUS_URL</span>/pythonpkgs/ConsensusCore2-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ConsensusCore2_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-cp27-cp27mu-linux_x86_64</span>.whl</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"> curl <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">--upload-file</span> dist/GenomicConsensus-<span class="k" style="font-weight: 600;">*</span>.whl <span class="nv" style="color: #008080;">$NEXUS_URL</span>/pythonpkgs/GenomicConsensus-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GenomicConsensus_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-cp27-cp27mu-linux_x86_64</span>.whl</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> bamboo_artifacts</span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> bamboo_artifacts/gcc-6.4.0/wheelhouse</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>_deps/ConsensusCore/dist/ConsensusCore-<span class="k" style="font-weight: 600;">*</span>.whl bamboo_artifacts/gcc-6.4.0/wheelhouse/ConsensusCore-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ConsensusCore_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-cp27-cp27mu-linux_x86_64</span>.whl</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>_deps/unanimity/ConsensusCore2-<span class="k" style="font-weight: 600;">*</span>.whl bamboo_artifacts/gcc-6.4.0/wheelhouse/ConsensusCore2-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ConsensusCore2_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-cp27-cp27mu-linux_x86_64</span>.whl</span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>dist/GenomicConsensus-<span class="k" style="font-weight: 600;">*</span>.whl bamboo_artifacts/gcc-6.4.0/wheelhouse/GenomicConsensus-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GenomicConsensus_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-cp27-cp27mu-linux_x86_64</span>.whl</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<li id="9ea7ba3e397712057afe008b4efa78e61af3d9cd">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#9ea7ba3e397712057afe008b4efa78e61af3d9cd"><strong>scripts/ci/setup.sh</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;">#!/usr/bin/env 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: #000080;">-vex</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#########</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># SETUP #</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#########</span></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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/mnt/software/p/python/wheelhouse/develop/"</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--find-links</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="k" style="font-weight: 600;">}</span> coverage <span class="s1" style="color: #d14;">'h5py<2.9'</span> nose numpy</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--find-links</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-e</span> _deps/pbcommand</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--find-links</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-e</span> _deps/pbcore</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--user</span> <span class="nt" style="color: #000080;">--find-links</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WHEELHOUSE</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-e</span> _deps/pbtestdata</span></pre>
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<li id="dc4d5d1220b0cd2b76cb436a076ddf99d8de0fdb">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#dc4d5d1220b0cd2b76cb436a076ddf99d8de0fdb"><strong>scripts/ci/test.sh</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;">#!/usr/bin/env 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: #000080;">-vex</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">########</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># TEST #</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">########</span></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="c" style="color: #998; font-style: italic;">## CC1 version test</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">python <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'import ConsensusCore; print ConsensusCore.Version.VersionString()'</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></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;">## CC2 version test</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">python <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'import ConsensusCore2; print ConsensusCore2.__version__'</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## test CC2 via GC</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">coverage run <span class="nt" style="color: #000080;">--source</span> GenomicConsensus <span class="nt" style="color: #000080;">-m</span> py.test <span class="nt" style="color: #000080;">--verbose</span> <span class="nt" style="color: #000080;">--junit-xml</span><span class="o" style="font-weight: 600;">=</span>nosetests.xml tests/unit</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"><span class="c" style="color: #998; font-style: italic;">## Run fairly fast cram tests</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">make basic-tests</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">bamboo_shortPlanName</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">==</span> GenomicConsensus-nightly <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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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## test GC</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> make unit-tests</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## test GC cram</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> make basic-tests</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## test GC extra</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> make extra-tests</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## test GC internal</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> make internal-tests</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;">fi</span></span></pre>
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<li id="17578dc0813a46c3b563d8bbc40c5360e1124b3e">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#17578dc0813a46c3b563d8bbc40c5360e1124b3e"><strong>scripts/nightly/build.sh</strong>
deleted
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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 -e</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;">echo</span> <span class="s2" style="color: #d14;">"# DEPENDENCIES"</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;">echo</span> <span class="s2" style="color: #d14;">"## Load modules"</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source</span> /mnt/software/Modules/current/init/bash</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell">module load git</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell">module load gcc</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell">module load python/2</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell">module load zlib</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell">module load cmake ninja</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell">module load swig ccache boost cram</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Get into virtualenv"</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> venv <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>virtualenv venv</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></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="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source </span>venv/bin/activate</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;">set</span> <span class="nt" style="color: #000080;">-vxeuo</span> pipefail</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Install pip modules</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--upgrade</span> pip</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install </span>cython pysam cram pytest coverage jsonschema avro nose <span class="nv" style="color: #008080;">numpy</span><span class="o" style="font-weight: 600;">==</span>1.14.5</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--no-deps</span> http://bitbucket:7990/rest/api/latest/projects/SL/repos/pbcommand/archive?format<span class="o" style="font-weight: 600;">=</span>zip</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--no-deps</span> http://bitbucket:7990/rest/api/latest/projects/SAT/repos/pbcore/archive?format<span class="o" style="font-weight: 600;">=</span>zip</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">### Get PacBioTestData</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> ../PacBioTestData <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd</span> .. <span class="o" style="font-weight: 600;">&&</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"> git clone https://github.com/PacificBiosciences/PacBioTestData.git <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd</span> ../PacBioTestData <span class="o" style="font-weight: 600;">&&</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> git lfs pull <span class="o" style="font-weight: 600;">&&</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"> make python <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Fetch unanimity submodules</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Bamboo's checkout of unanimity doesn't set the "origin" remote to</span></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;"># something meaningful, which means we can't resolve the relative</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># submodules. Override the remote here.</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd</span> ../unanimity <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"> git remote set-url origin ssh://git@bitbucket:7999/sat/unanimity.git <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"> git submodule update <span class="nt" style="color: #000080;">--init</span> <span class="nt" style="color: #000080;">--remote</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># BUILD</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## pip install CC2</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd</span> ../unanimity <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">CMAKE_BUILD_TYPE</span><span class="o" style="font-weight: 600;">=</span>ReleaseWithAssert <span class="nv" style="color: #008080;">CMAKE_COMMAND</span><span class="o" style="font-weight: 600;">=</span>cmake <span class="nv" style="color: #008080;">ZLIB_INCLUDE_DIR</span><span class="o" style="font-weight: 600;">=</span>/mnt/software/z/zlib/1.2.5/include <span class="nv" style="color: #008080;">ZLIB_LIBRARY</span><span class="o" style="font-weight: 600;">=</span>/mnt/software/z/zlib/1.2.5/lib/libz.so <span class="nv" style="color: #008080;">VERBOSE</span><span class="o" style="font-weight: 600;">=</span>1 pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--verbose</span> <span class="nt" style="color: #000080;">--upgrade</span> <span class="nt" style="color: #000080;">--no-deps</span> <span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## install ConsensusCore</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">cd</span> ../ConsensusCore <span class="o" style="font-weight: 600;">&&</span> python setup.py <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--boost</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BOOST_ROOT</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## install GC</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"><span class="o" style="font-weight: 600;">(</span> pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">--upgrade</span> <span class="nt" style="color: #000080;">--no-deps</span> <span class="nt" style="color: #000080;">--verbose</span> <span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">)</span></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;">set</span> +u</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell">deactivate</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-u</span></span></pre>
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<li id="3dba9412adb7094797d775feafcd655f24bb726c">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#3dba9412adb7094797d775feafcd655f24bb726c"><strong>scripts/nightly/test.sh</strong>
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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 -e</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;">echo</span> <span class="s2" style="color: #d14;">"# DEPENDENCIES"</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;">echo</span> <span class="s2" style="color: #d14;">"## Load modules"</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source</span> /mnt/software/Modules/current/init/bash</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell">module load git</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell">module load gcc</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell">module load python/2</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell">module load zlib</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell">module load cmake ninja</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell">module load swig ccache boost cram</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell">module load cram</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell">module load mummer</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell">module load exonerate/2.0.0</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">module load blasr/2.3.0</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">module load gfftools/dalexander</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"><span class="nb" style="color: #0086b3;">source </span>venv/bin/activate</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-vxeuo</span> pipefail</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># TEST</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## CC2 version test</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">python <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"import ConsensusCore2 ; print ConsensusCore2.__version__"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## To use .cmp.h5, pbcore needs h5py.</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell">pip <span class="nb" style="color: #0086b3;">install </span>h5py</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## test GC</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell">make unit-tests</span>
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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;">## test GC cram</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell">make basic-tests</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## test GC extra</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell">make extra-tests</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## test GC internal</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell">make internal-tests</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> +u</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell">deactivate</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-u</span></span></pre>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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">@@ -11,10 +11,10 @@ from os.path import join, dirname</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GenomicConsensus'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.3.<span class="idiff left right">2</span>'</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># don't forget to update GenomicConsensus/__init__.py and doc/conf.py too</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.3.<span class="idiff left right">3</span>'</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># don't forget to update GenomicConsensus/__init__.py and doc/conf.py too</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Pacific Biosciences'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'devnet@pacificbiosciences.com'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'LICENSE<span class="idiff left right">S</span>'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'LICENSE'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'bin/variantCaller'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'bin/summarizeConsensus'</span><span class="p">,</span></span>
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<li id="80753364ed500dbeacc378880ea8eacc86b0ccc3">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#80753364ed500dbeacc378880ea8eacc86b0ccc3"><strong>tests/cram/arrow-all4mer-diploid.t</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">@@ -6,7 +6,7 @@ Test Arrow diploid polishing</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="nv" style="color: #008080;">Run</span> <span class="nv" style="color: #008080;">arrow</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">arrow</span> <span class="nv" style="color: #008080;">$INPUT</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">r</span> <span class="nv" style="color: #008080;">$REFERENCE</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">diploid</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">o</span> <span class="nv" style="color: #008080;">dipl</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">vcf</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">o</span> <span class="nv" style="color: #008080;">cons</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fasta</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">arrow</span> <span class="nv" style="color: #008080;">$INPUT</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">r</span> <span class="nv" style="color: #008080;">$REFERENCE</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">diploid</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">o</span> <span class="nv" style="color: #008080;">dipl</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">vcf</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">o</span> <span class="nv" style="color: #008080;"><span class="idiff left">dipl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">gff</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">o</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">cons</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fasta</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="nv" style="color: #008080;">Perfect</span> <span class="nv" style="color: #008080;">diploid</span> <span class="nv" style="color: #008080;">polishing</span><span class="p">,</span> <span class="nv" style="color: #008080;">found</span> <span class="nv" style="color: #008080;">all</span> <span class="nv" style="color: #008080;">variants</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"></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">@@ -28,3 +28,13 @@ Ambiguous-free consensus sequence</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"> <span class="nv" style="color: #008080;">AGTAGGTGCTGTCGAGCGGCAGCTAGCGGTCAATTCTATGACCTCGTTGCGTACTCCGAA</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"> <span class="nv" style="color: #008080;">TCATTGAGCAACCGTCTTTGGTAAATACGAGTTCAGGCAAGCTTGCTGAGGACTAGTAGC</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"> <span class="nv" style="color: #008080;">T</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="nv" style="color: #008080;">TAG</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3610</span><span class="p">:</span> <span class="nv" style="color: #008080;">test</span> <span class="nv" style="color: #008080;">that</span> <span class="p">`</span><span class="sb" style="color: #d14;">gffToBed</span><span class="p">`</span> <span class="nv" style="color: #008080;">actually</span> <span class="nv" style="color: #008080;">works</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">gffToBed</span> <span class="nv" style="color: #008080;">coverage</span> <span class="nv" style="color: #008080;">dipl</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">gff</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="nv" style="color: #008080;">track</span> <span class="nv" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">variants</span> <span class="nv" style="color: #008080;">description</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">PacBio: snps, insertions, and deletions derived from consensus calls against reference</span><span class="p">"</span> <span class="nv" style="color: #008080;">useScore</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="nv" style="color: #008080;">all4merDipl</span> <span class="mi" style="color: #099;">27</span> <span class="mi" style="color: #099;">28</span> <span class="nv" style="color: #008080;">meanCov</span> <span class="mf" style="color: #099;">100.000</span> <span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"> <span class="nv" style="color: #008080;">all4merDipl</span> <span class="mi" style="color: #099;">70</span> <span class="mi" style="color: #099;">71</span> <span class="nv" style="color: #008080;">meanCov</span> <span class="mf" style="color: #099;">100.000</span> <span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"> <span class="nv" style="color: #008080;">all4merDipl</span> <span class="mi" style="color: #099;">127</span> <span class="mi" style="color: #099;">128</span> <span class="nv" style="color: #008080;">meanCov</span> <span class="mf" style="color: #099;">100.000</span> <span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"> <span class="nv" style="color: #008080;">all4merDipl</span> <span class="mi" style="color: #099;">193</span> <span class="mi" style="color: #099;">194</span> <span class="nv" style="color: #008080;">meanCov</span> <span class="mf" style="color: #099;">100.000</span> <span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="nv" style="color: #008080;">all4merDipl</span> <span class="mi" style="color: #099;">247</span> <span class="mi" style="color: #099;">248</span> <span class="nv" style="color: #008080;">meanCov</span> <span class="mf" style="color: #099;">100.000</span> <span class="o" style="font-weight: 600;">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#fc0f82229e23cec09bfca2c1e4dfde6124135457"><strong>tests/cram/internal/quiver-ecoli.t</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">@@ -35,11 +35,14 @@ since I built the new reference.</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"><span class="s1" style="color: #d14;"> ecoliK12_pbi_March2013 . insertion 1536 1536 . . . reference=.;variantSeq=C;coverage=91;confidence=47</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"><span class="s1" style="color: #d14;"> $ cat variants.vcf | untabify</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##fileformat=VCFv4.<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##fileformat=VCFv4.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##fileDate=* (glob)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##source=GenomicConsensusV* (glob)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##reference=file://* (glob)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##contig=<ID=ecoliK12_pbi_March2013,length=4642522></span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##FILTER=<ID=q40,Description="Quality below 40"></span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##FILTER=<ID=c5,Description="Coverage below 5"></span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="perl"><span class="s1" style="color: #d14;"> #CHROM POS ID REF ALT QUAL FILTER INFO</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"><span class="s1" style="color: #d14;"> ecoliK12_pbi_March2013 84 . TG T 48 PASS DP=53</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"><span class="s1" style="color: #d14;"> ecoliK12_pbi_March2013 218 . GA G 47 PASS DP=58</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#92b57ec44fc684442554c3d517b59da4ec8964b2"><strong>tests/cram/quiver-noqvs-test.t</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">@@ -26,12 +26,13 @@ I'm not all that surprised.</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"><span class="s1" style="color: #d14;"> 3primeEnd . deletion 369 369 . . . reference=G;variantSeq=.;coverage=83;confidence=6</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="s1" style="color: #d14;"> $ cat v.vcf | tr </span><span class="p">'</span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">t</span><span class="p">'</span><span class="s1" style="color: #d14;"> </span><span class="p">'</span> <span class="p">'</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##fileformat=VCFv4.<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##fileformat=VCFv4.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##fileDate=* (glob)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##source=GenomicConsensusV* (glob)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##reference=file://* (glob)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##contig=<ID=5primeEnd,length=156></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##contig=<ID=3primeEnd,length=386></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="s1" style="color: #d14;"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"><span class="s1" style="color: #d14;"> #CHROM POS ID REF ALT QUAL FILTER INFO</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"><span class="s1" style="color: #d14;"> 3primeEnd 295 . TG T 4 PASS DP=92</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"><span class="s1" style="color: #d14;"> 3primeEnd 368 . AG A 6 PASS DP=83</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#f37b7319b5fc970aa5502c7a9001ef404e6ec91d"><strong>tests/cram/version.t</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">@@ -2,7 +2,7 @@ This actually failed once because of a missing import, so we might as</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="nv" style="color: #008080;">well</span> <span class="nv" style="color: #008080;">test</span> <span class="nv" style="color: #008080;">it</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">variantCaller</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">version</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="perl"> <span class="mf" style="color: #099;">2.3.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"> <span class="mf" style="color: #099;">2.3.<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="nv" style="color: #008080;">This</span> <span class="nv" style="color: #008080;">will</span> <span class="nv" style="color: #008080;">break</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">parser</span> <span class="nv" style="color: #008080;">setup</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">messed</span> <span class="nv" style="color: #008080;">up</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/a0579e221faf1669906b71b777d7e68fa5d8c258#ba6ee8ca3889715aebcca9ac8140282add1ca6ed"><strong>tests/unit/test_summarize_consensus.py</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">@@ -31,7 +31,7 @@ chr2\t.\tregion\t10000\t23469\t0.00\t+\t.\tcov=0,48,89;cov2=47.303,12.036;gaps=1</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;">chr3</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">region</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7000</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.00</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">cov=0,48,89;cov2=47.303,12.036;gaps=1,24"""</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">EXPECTED</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">##source GenomicConsensus 2.3.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">##source GenomicConsensus 2.3.<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">##pacbio-alignment-summary-version 0.6</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">##source-commandline this line will be skipped in the comparison</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">region</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5000</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0.00</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">cov=4,23,28;cov2=20.162,5.851;gaps=0,0;cQv=20,20,20;del=0;ins=0;sub=1</span></span>
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