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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/paleomix">Debian Med / paleomix</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/72ba208593659a0b54c21dce9730e7dd3a7e8c84">72ba2085</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:45:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.14</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/eec7559283e9e292dd9167bb7fb0ae9f4df4144e">eec75592</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:45:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/36e02f07a2843ad33fd69011b0010542b36f5965">36e02f07</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:45:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.14'
Update to upstream version '1.2.14'
with Debian dir 85aa9709385c29641b2799a674ae563d0360c88c</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/8e4c0e55447cbf148970a1fefe10698dadb5d866">8e4c0e55</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:45:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/c9edf29558a7fc4af2bf2a8f103cb7ad3506f6af">c9edf295</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:45:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/a55a44c427ae2965048ed492ff93e31874a382f2">a55a44c4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:46:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/a41e449aa32d7f9b454f4214789353391765dfac">a41e449a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T07:57:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/d494bff3f643877763c516b132b22a2331cc0dc3">d494bff3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T08:08:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add TODO
</pre>
</li>
</ul>
<h4>20 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
</a>
</li>
<li class="file-stats">
<a href="#31db6545668043f26d9d05b8338b53acf3b3c5e1">
paleomix/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#16f4428581f539a85da5bb899c2adbf757a61024">
paleomix/nodes/gatk.py
</a>
</li>
<li class="file-stats">
<a href="#82233c75268e15a595a90e8494933e20039bfa91">
paleomix/nodes/picard.py
</a>
</li>
<li class="file-stats">
<a href="#80fcdaee65ee5b165a4ad08c84a9b033d5a46812">
paleomix/tools/bam_pipeline/nodes.py
</a>
</li>
<li class="file-stats">
<a href="#3e141c37cd17467d2228e9ff9f0a3925ece2970e">
paleomix/tools/zonkey/build_tped.py
</a>
</li>
<li class="file-stats">
<a href="#d5069f460f104fd4f0871267184bdf7a7c2c69dc">
paleomix/tools/zonkey/common.py
</a>
</li>
<li class="file-stats">
<a href="#98bbb46114dc187c6d3230b0201d14d1ad22be9b">
paleomix/tools/zonkey/config.py
</a>
</li>
<li class="file-stats">
<a href="#3f48743b06ecd99cd7a9c238ad900ffc5618d66f">
paleomix/tools/zonkey/database.py
</a>
</li>
<li class="file-stats">
<a href="#d7867c6c7f20d83e953476106ea42fb8f456d6d8">
paleomix/tools/zonkey/parts/admixture.py
</a>
</li>
<li class="file-stats">
<a href="#ff57991cd83aa3cf80b39abb4266afbf51716631">
paleomix/tools/zonkey/parts/common.py
</a>
</li>
<li class="file-stats">
<a href="#07661fb9d6b06c26141694495c4ad1703ea3de7a">
paleomix/tools/zonkey/parts/nuclear.py
</a>
</li>
<li class="file-stats">
<a href="#952029038f001015c0d133ad89bf6add98045448">
paleomix/tools/zonkey/parts/report.py
</a>
</li>
<li class="file-stats">
<a href="#a4ca0c984f1c357ecc12750d6ee9964c69e69104">
paleomix/tools/zonkey/parts/summary.py
</a>
</li>
<li class="file-stats">
<a href="#bdd39bf22335b3c612da534e11b43abc4f368d2b">
paleomix/tools/zonkey/pipeline.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="diff-line-num new_line" data-linenumber="1" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
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<td class="diff-line-num new_line" data-linenumber="2" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.14] - 2019-12-01</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Changed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p"> -</span> Improved handling of K-groups in zonkey database files</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="markdown"><span class="p"> -</span> Change BAM pipeline version requirement for GATK to < v4.0, as the</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="markdown"> the Indel Realigner has been removed in GATK v4.0</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="markdown"><span class="p"> -</span> Fixed version detection of GATK for v4.0 (issue #23)</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.8] - 2019-10-27</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Changed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="markdown"><span class="p"> -</span> Zonkey now identifies nuclear chromosomes by size instead of name; this</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"> is done to better handle FASTAs downloaded from different sources</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.7] - 2019-10-15</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p"> -</span> Fixed handling of digit only chromosome names in Zonkey</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p"> -</span> Remove dashes from Zonkey MT genomes when running 'mito' command</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.6] - 2019-10-13</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p"> -</span> Handle .<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>miss files created by some versions of plink in Zonkey</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.5] - 2019-09-29</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p"> -</span> Ignore ValidateSamFile warning REF_SEQ_TOO_LONG_FOR_BAI warning when</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"> processing genomes with contigs too large for BAI index files.</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="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.4] - 2019-03-25</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p"> -</span> Improved detection of Picard versions in cases where 'java'</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="587" 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="620" 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">@@ -587,7 +620,12 @@ the (partially) updated documentation now hosted on ReadTheDocs.</td>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="markdown"><span class="p"> -</span> Switching to more traditional version-number tracking.</span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="markdown"></span>
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="markdown"></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Unreleased</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...HEAD</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Unreleased</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.14...HEAD</span></span>
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<td class="diff-line-num new new_line" data-linenumber="624" 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">
624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.14</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.8...v1.2.14</span></span>
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<td class="diff-line-num new new_line" data-linenumber="625" 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="LC625" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.8</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.7...v1.2.13.8</span></span>
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<td class="diff-line-num new new_line" data-linenumber="626" 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">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.7</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.6...v1.2.13.7</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.6</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.5...v1.2.13.6</span></span>
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<td class="diff-line-num new new_line" data-linenumber="628" 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">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.5</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...v1.2.13.5</span></span>
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591
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.4</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...v1.2.13.4</span></span>
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592
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.3</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3</span></span>
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593
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631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.2</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2</span></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">paleomix (1.2.1<span class="idiff left right">3.</span>4-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">paleomix (1.2.14-1) UNRELEASED; urgency=medium</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></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="plaintext"> * New upstream version</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * debhelper-compat 12</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> TODO: see https://github.com/MikkelSchubert/paleomix/issues/15</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Set upstream metadata fields: Repository, Repository-Browse.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> TODO: Python3 port see</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> https://github.com/MikkelSchubert/paleomix/issues/15</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 11 Sep 2019 11:21:12 +02</span>00</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Tue, 17 Dec 2019 08:45:11 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">paleomix (1.2.13.3-1) unstable; urgency=medium</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> default-jre-headless,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> bowtie2,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> rsync</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/paleomix</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/paleomix.git</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Homepage: https://geogenetics.ku.dk/publications/paleomix</span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,14 +3,14 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"paleomix"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="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;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></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;"># trap "rm -rf $A<span class="idiff left right">DT</span>TMP" 0 INT QUIT ABRT PIPE TERM</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></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;"># trap "rm -rf $A<span class="idiff left right">UTOPKGTEST_</span>TMP" 0 INT QUIT ABRT PIPE TERM</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/tests <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/tests <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>gz <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span><span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># fasta_file.fasta.gz needs to stay compressed for testing</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: ></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Mikkel Schubert and Luca Ermini and Clio Der Sarkissian and Hákon Jónsson and</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Aurélien Ginolhac and Robert Schaefer and Michael D Martin and Ruth Fernández</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> and Martin Kircher and Molly McCue and Eske Willerslev and Ludovic Orlando</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Characterization of ancient and modern genomes by SNP detection and</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> phylogenomic and metagenomic analysis using PALEOMIX</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Journal: Nature Protocols</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Year: 2014</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Volume: 9</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> Number: 5</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> Pages: 1056-82</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> DOI: 10.1038/nprot.2014.063</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> PMID: 24722405</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> URL: http://www.nature.com/nprot/journal/v9/n5/full/nprot.2014.063.html</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> <span class="idiff left right"> </span>Author: ></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Mikkel Schubert and Luca Ermini and Clio Der Sarkissian and Hákon Jónsson and</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>Aurélien Ginolhac and Robert Schaefer and Michael D Martin and Ruth Fernández</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>and Martin Kircher and Molly McCue and Eske Willerslev and Ludovic Orlando</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: ></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Characterization of ancient and modern genomes by SNP detection and</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>phylogenomic and metagenomic analysis using PALEOMIX</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Nature Protocols</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2014</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 9</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 5</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 1056-82</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1038/nprot.2014.063</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 24722405</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://www.nature.com/nprot/journal/v9/n5/full/nprot.2014.063.html</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Registry:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> Entry: OMICS_03749</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - Name: SciCrunch</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> Entry: SCR_015057</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> Entry: PALEOMIX</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> Entry: NA</span></pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Entry: OMICS_03749</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: SCR_015057</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Entry: PALEOMIX</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Repository: https://github.com/MikkelSchubert/paleomix.git</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Repository-Browse: https://github.com/MikkelSchubert/paleomix</span></pre>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.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">@@ -57,7 +57,7 @@ author = u'Mikkel Schubert'</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version.</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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;">u'1.2'</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags.</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'1.2.1<span class="idiff left right">3</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'1.2.1<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for a list of supported languages.</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#31db6545668043f26d9d05b8338b53acf3b3c5e1"><strong>paleomix/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># SOFTWARE.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">__version_info__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1<span class="idiff left">3</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" 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;"><span class="idiff left">'</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">i.</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">i.</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">i.</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">i'</span></span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version_info__</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">__version_info__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1<span class="idiff left right">4</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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;"><span class="idiff left">"</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">i.</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">i.</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">i"</span></span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version_info__</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>
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<pre style="margin: 0;"> <span id="LC28" 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="n" style="color: #333;">command</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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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#16f4428581f539a85da5bb899c2adbf757a61024"><strong>paleomix/nodes/gatk.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">@@ -45,6 +45,9 @@ from paleomix.nodes.bwa import \</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">paleomix.common.versions</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">versions</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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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="n" style="color: #333;">_RE_GATK_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">r"^(?:The Genome Analysis Toolkit \(GATK\) v)?(\d+)\.(\d+)"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_gatk_version_check</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"""Returns a version-check object for the "GenomeAnalysisTK.jar" located at</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> config.jar_root; for now, this check only serves to verify that the JAR can</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">@@ -60,8 +63,8 @@ def _get_gatk_version_check(config):</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Any version is fine; for now just catch old JREs</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Requirement</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">finalized_call</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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;">"GenomeAnalysisTK"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">search</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">r"^(\d+)\.(\d+)"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">checks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">Any</span></span><span class="p"><span class="idiff right">(</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">search</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left right">_RE_GATK_VERSION</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">checks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">LT</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">_GATK_VERSION</span><span class="p">[</span><span class="n" style="color: #333;">jar_file</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">requirement</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_GATK_VERSION</span><span class="p">[</span><span class="n" style="color: #333;">jar_file</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;">_GATK_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<li id="82233c75268e15a595a90e8494933e20039bfa91">
<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#82233c75268e15a595a90e8494933e20039bfa91"><strong>paleomix/nodes/picard.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">@@ -60,10 +60,13 @@ class PicardNode(CommandNode):</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ValidateBAMNode</span><span class="p">(</span><span class="n" style="color: #333;">PicardNode</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC62" 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;">config</span><span class="p">,</span> <span class="n" style="color: #333;">input_bam</span><span class="p">,</span> <span class="n" style="color: #333;">input_index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">output_log</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="LC63" class="line" lang="python"> <span class="n" style="color: #333;">ignored_checks</span><span class="o" style="font-weight: 600;">=</span><span class="p">(),</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">ignored_checks</span><span class="o" style="font-weight: 600;">=</span><span class="p">(),</span> <span class="n" style="color: #333;"><span class="idiff left">big_genome_mode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">builder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">picard_command</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="s" style="color: #d14;">"ValidateSamFile"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">_set_max_open_files</span><span class="p">(</span><span class="n" style="color: #333;">builder</span><span class="p">,</span> <span class="s" style="color: #d14;">"MAX_OPEN_TEMP_FILES"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></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="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">big_genome_mode</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;">_configure_for_big_genome</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">builder</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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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="s" style="color: #d14;">"I"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%(IN_BAM)</span><span class="s" style="color: #d14;">s"</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">check</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ignored_checks</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"IGNORE"</span><span class="p">,</span> <span class="n" style="color: #333;">check</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"="</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 +82,22 @@ class ValidateBAMNode(PicardNode):</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dependencies</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_configure_for_big_genome</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">builder</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CSI uses a different method for assigning BINs to records, which</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Picard currently does not support.</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"IGNORE"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INVALID_INDEXING_BIN"</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span></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="n" style="color: #333;">jar_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">jar_root</span><span class="p">,</span> <span class="n" style="color: #333;">_PICARD_JAR</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">version_check</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_PICARD_VERSION_CACHE</span><span class="p">[</span><span class="n" style="color: #333;">jar_path</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" 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="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">version_check</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">19</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Useless warning, as we do not build BAI indexes for large genomes</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"IGNORE"</span><span class="p">,</span> <span class="s" style="color: #d14;">"REF_SEQ_TOO_LONG_FOR_BAI"</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">VersionRequirementError</span><span class="p">:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># Ignored here, handled elsewhere</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BuildSequenceDictNode</span><span class="p">(</span><span class="n" style="color: #333;">PicardNode</span><span class="p">):</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" 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;">config</span><span class="p">,</span> <span class="n" style="color: #333;">reference</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</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">@@ -247,7 +266,8 @@ def picard_command(config, command):</td>
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247
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AtomicJavaCmdBuilder</span><span class="p">(</span><span class="n" style="color: #333;">jar_path</span><span class="p">,</span></span>
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248
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">temp_root</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_root</span><span class="p">,</span></span>
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249
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">jre_options</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">jre_options</span><span class="p">,</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">CHECK_JAR</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">CHECK_JAR</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">version</span><span class="p">,</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">set_cwd</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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251
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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252
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"></span>
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253
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">params</span></span>
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<li id="80fcdaee65ee5b165a4ad08c84a9b033d5a46812">
<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#80fcdaee65ee5b165a4ad08c84a9b033d5a46812"><strong>paleomix/tools/bam_pipeline/nodes.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">@@ -43,15 +43,11 @@ def index_and_validate_bam(config, prefix, node, log_file=None,</td>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># where high-quality reads may cause mis-identification of qualities</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"INVALID_QUALITY_FORMAT"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">'IndexFormat'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'.csi'</span><span class="p">:</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CSI uses a different method for assigning BINs to records, which</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Picard currently does not support.</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">ignored_checks</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"INVALID_INDEXING_BIN"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ValidateBAMNode</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">input_bam</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">input_index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">index_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">ignored_checks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ignored_checks</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">big_genome_mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"IndexFormat"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".csi"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">output_log</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">node</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#3e141c37cd17467d2228e9ff9f0a3925ece2970e"><strong>paleomix/tools/zonkey/build_tped.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">@@ -258,9 +258,10 @@ def write_summary(args, filename, statistics):</td>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">statistics</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="s" style="color: #d14;">"MISSING"</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_bam</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">bam_handle</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_bam</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">bam_handle</span><span class="p">,</span> <span class="n" style="color: #333;">mapping</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">reverse_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">mapping</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">mapping</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">raw_references</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">references</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">references</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">common</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">contig_name_to_plink_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_references</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">references</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">reverse_mapping</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_references</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">downsample</span><span class="p">:</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Downsampling to at most </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i BAM records ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -343,7 +344,7 @@ def main(argv):</td>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"> <span class="s" style="color: #d14;">"identifiable nuclear alignments.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">process_bam</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">bam_handle</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">process_bam</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">bam_handle</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bam_info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nuclear_contigs</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#d5069f460f104fd4f0871267184bdf7a7c2c69dc"><strong>paleomix/tools/zonkey/common.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">@@ -56,7 +56,7 @@ def contig_name_to_plink_name(chrom):</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> identified.</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">upper</span></span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chrom</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"XY"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"chr"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">chrom</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#98bbb46114dc187c6d3230b0201d14d1ad22be9b"><strong>paleomix/tools/zonkey/config.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">@@ -218,14 +218,14 @@ def _process_samples(config):</td>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">"mitochondrial BAM specified; the mitochondrial "</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">"genome in the first BAM will not be used!"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="s" style="color: #d14;">"Nuc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">filename</span></span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="s" style="color: #d14;">"Nuc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"Path"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Info"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filetype</span></span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">"Mito"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_nuclear</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Nuc"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Two nuclear BAMs specified!"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="s" style="color: #d14;">"Nuc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">filename</span></span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="s" style="color: #d14;">"Nuc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"Path"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Info"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filetype</span></span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_mitochondrial</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Mito"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Two nuclear BAMs specified!"</span><span class="p">)</span></span>
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<li id="3f48743b06ecd99cd7a9c238ad900ffc5618d66f">
<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#3f48743b06ecd99cd7a9c238ad900ffc5618d66f"><strong>paleomix/tools/zonkey/database.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">@@ -19,7 +19,9 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># SOFTWARE.</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tarfile</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</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">@@ -46,14 +48,14 @@ _SETTINGS_KEYS = ('Format', 'Revision', 'Plink', 'NChroms', 'MitoPadding',</td>
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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="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BAMInfo</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC50" 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>
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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;">nuclear</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></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;">nuclear<span class="idiff left">_contigs</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{}</span></span></span>
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<pre style="margin: 0;"> <span id="LC52" 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;">mt_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></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;">mt_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</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;">mt_padding</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_nuclear</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="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nuclear</span></span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nuclear_contigs</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_mitochondrial</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -62,7 +64,7 @@ class BAMInfo(object):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC65" class="line" lang="python"> <span class="n" style="color: #333;">tmpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BAMInfo(nuclear=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r, mt_contig=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r, mt_length=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r, mt_padding=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r)"</span></span>
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<pre style="margin: 0;"> <span id="LC66" 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;">return</span> <span class="n" style="color: #333;">tmpl</span> <span class="o" style="font-weight: 600;">%</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;">nuclear</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;">mt_contig</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;">return</span> <span class="n" style="color: #333;">tmpl</span> <span class="o" style="font-weight: 600;">%</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;">nuclear<span class="idiff left right">_contigs</span></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;">mt_contig</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;">mt_length</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;">mt_padding</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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<pre style="margin: 0;"> <span id="LC70" 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">@@ -74,9 +76,10 @@ _SUPPORTED_DB_FORMAT_MINOR = 20160112</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Required columns in the 'contigs.txt' table; additional columns are ignored</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="n" style="color: #333;">_CONTIGS_TABLE_COLUMNS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">((</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Size'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Checksum'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Required columns in the 'samples.txt' table; additional columns are ignored</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="n" style="color: #333;">_SAMPELS_TABLE_COLUMNS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">((</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Group(2)'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Group(3)'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Species'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">'Sex'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SampleID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Publication'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Required columns in the 'samples.txt' table; additional non-group columns are ignored</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="n" style="color: #333;">_SAMPLES_TABLE_COLUMNS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">((</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Sex'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SampleID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Publication'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Regular expression for parsing Group(K) columns in samples.txt</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><span class="n" style="color: #333;">_SAMPLES_TABLE_GROUP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'^Group\((?P<K>.+)\)$'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"></span>
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81
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ZonkeyDBError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" 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="106" 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">@@ -103,7 +106,7 @@ class ZonkeyDB(object):</td>
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103
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">print_info</span><span class="p">(</span><span class="s" style="color: #d14;">' - Reading list of contigs ...'</span><span class="p">)</span></span>
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104
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107
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<pre style="margin: 0;"> <span id="LC107" 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;">contigs</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;">_read_contigs_table</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"contigs.txt"</span><span class="p">)</span></span>
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105
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">print_info</span><span class="p">(</span><span class="s" style="color: #d14;">' - Reading list of samples ...'</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" 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;">samples</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;">_read_samples_table</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"samples.txt"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" 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;">samples</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">groups</span></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;">_read_samples_table</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"samples.txt"</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">print_info</span><span class="p">(</span><span class="s" style="color: #d14;">' - Reading mitochondrial sequences ...'</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;"> <span id="LC111" 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;">mitochondria</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;">_read_mitochondria</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span></span>
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109
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">"mitochondria.fasta"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" 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="199" 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">@@ -196,7 +199,7 @@ class ZonkeyDB(object):</td>
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196
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read_samples_table</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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197
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_check_required_file</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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198
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_table</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"samples.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_table</span><span class="p">(</span><span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"samples.txt"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_SAMPLES_TABLE_COLUMNS</span></span><span class="p">)</span></span>
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200
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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201
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: No samples found in genotypes table!"</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" 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="209" 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">@@ -206,16 +209,42 @@ class ZonkeyDB(object):</td>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">"expected 'MALE', 'FEMALE', or 'NA'"</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Sex"</span><span class="p">],))</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">k_groups</span><span class="p">,)</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"The </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r column in the samples table must "</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="s" style="color: #d14;">"either contain </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i ancestral groups, or "</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"none"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samples</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">group_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_SAMPLES_TABLE_GROUP</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">k_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupdict</span><span class="p">()[</span><span class="s" style="color: #d14;">"K"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">k_value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"Malformed Group column name; K is "</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">"not a number: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,))</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">k_value</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">7</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"K must be between 2 and 7, but found </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r"</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,))</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">group_keys</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">k_value</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">k_value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_keys</span><span class="p">:</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample_key</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">[</span><span class="n" style="color: #333;">sample_key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">group_labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">(</span><span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group_labels</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">):</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># Allowed for backwards compatibility</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'-'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_labels</span><span class="p">:</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"Not all samples column </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r assignd a group"</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,))</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">group_labels</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">k_value</span><span class="p">:</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i groups in column </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r, found </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i"</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">k_value</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">group_labels</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">k_value</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">groups</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">"No valid groups in samples.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">groups</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read_sample_order</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">tar_handle</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" 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">@@ -390,9 +419,7 @@ class ZonkeyDB(object):</td>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">linenum</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'Sample1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Sample2'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">group_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">'K'</span><span class="p">],)</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">group_key</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">frozenset</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;">groups</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"K"</span><span class="p">])]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>
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396
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'-'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ZonkeyDBError</span><span class="p">(</span><span class="s" style="color: #d14;">'Invalid group in column </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r in '</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">@@ -508,38 +535,44 @@ def _validate_mito_bam(data, handle, info):</td>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_nuclear_bam</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">handle</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check that chromosomes are of expected size; unused chroms are ignored.</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">bam_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">contig_name_to_plink_name</span><span class="p">,</span> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">references</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lengths</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">ref_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigs</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">contigs_found</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">ref_contigs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bam_contigs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">contigs_found</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">bam_contigs</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"Size"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Chrom </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r in the BAM does not match the "</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="s" style="color: #d14;">"length specified in data file:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"> <span class="s" style="color: #d14;">" - Expected: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="s" style="color: #d14;">" - Found: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i"</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">bam_contigs</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">],</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"Size"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC528" 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="LC529" class="line" lang="python"> <span class="n" style="color: #333;">contigs_found</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">contigs_found</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">contigs_found</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Not all nuclear chromosomes found in BAM:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">ref_contigs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">is_found</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Found"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contigs_found</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"Not found!"</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">" - </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </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="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">is_found</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC539" 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="LC540" 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;">nuclear</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Match reference panel contigs with BAM contigs; identification is done</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># by size since different repositories use different naming schemes.</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">bam_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">length</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lengths</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">bam_contigs</span><span class="p">[</span><span class="n" style="color: #333;">length</span><span class="p">]</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;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">panel_names_to_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="n" style="color: #333;">bam_contig_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_contigs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"Size"</span><span class="p">],</span> <span class="p">())</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bam_contig_names</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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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">panel_names_to_bam</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_contig_names</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bam_contig_names</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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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">candidates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bam_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bam_contig_names</span><span class="p">:</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contig_name_to_plink_name</span><span class="p">(</span><span class="n" style="color: #333;">bam_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name</span><span class="p">:</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">candidates</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;">bam_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">candidates</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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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">panel_names_to_bam</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">print_warn</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">WARNING: Multiple candidates for chr</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s with size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i:"</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"Size"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bam_contig_names</span><span class="p">:</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">print_warn</span><span class="p">(</span><span class="s" style="color: #d14;">" - </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,))</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">panel_names_to_bam</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC565" 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;">nuclear_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">panel_names_to_bam</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">panel_names_to_bam</span><span class="p">:</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Not all nuclear chromosomes found in BAM:"</span><span class="p">)</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">()):</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">is_found</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"OK"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">panel_names_to_bam</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"Not found!"</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">" - </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </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="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">is_found</span><span class="p">))</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" 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="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_file_compression</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#d7867c6c7f20d83e953476106ea42fb8f456d6d8"><strong>paleomix/tools/zonkey/parts/admixture.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">@@ -36,7 +36,6 @@ class AdmixtureError(RuntimeError):</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_admixture_results</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CUTOFF</span><span class="p">):</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">k_groups</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;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_order</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="s" style="color: #d14;">"-"</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;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_admixture_read_results</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">_admixture_validate_ancestral_groups</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</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">@@ -46,7 +45,7 @@ def read_admixture_results(filename, data, k_groups, cutoff=CUTOFF):</td>
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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;">sample</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'-'</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;">continue</span></span>
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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="LC49" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">samples</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">sample</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">groups</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">k_groups</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff right">sample</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">cutoff</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">ancestral_groups</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">group</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">@@ -146,16 +145,13 @@ def _admixture_read_results(filename, samples):</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_admixture_validate_ancestral_groups</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">k_groups</span><span class="p">,)</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="p">[</span><span class="n" style="color: #333;">sample</span><span class="p">][</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">cutoff</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">k_groups</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">cutoff</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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159
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>
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160
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">mixed_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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161
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">memberships</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">()):</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#ff57991cd83aa3cf80b39abb4266afbf51716631"><strong>paleomix/tools/zonkey/parts/common.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">@@ -34,6 +34,7 @@ _DEFAULT_COLORS = ("#E69F00", "#56B4E9",</td>
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34
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WriteSampleList</span><span class="p">(</span><span class="n" style="color: #333;">Node</span><span class="p">):</span></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" 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;">config</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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36
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36
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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;">_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span></span>
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37
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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;">_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span></span>
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37
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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38
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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39
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<WriteSampleList -> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">output_file</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">@@ -44,17 +45,18 @@ class WriteSampleList(Node):</td>
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<pre style="margin: 0;"> <span id="LC45" 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 class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">temp</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">,</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;">output_files</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">samples</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;">_samples</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(3)"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">colors</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="n" style="color: #333;">_DEFAULT_COLORS</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="n" style="color: #333;">group</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;">_groups</span><span class="p">[</span><span class="nb" style="color: #0086b3;">max</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;">_groups</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">group_colors</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">())),</span> <span class="n" style="color: #333;">_DEFAULT_COLORS</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reroot_path</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Name</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Group</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Color</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">samples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">iteritems</span></span><span class="p"><span class="idiff right">()</span>):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Group(3)"</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">color</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">colors</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">group</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">sample_name</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">samples</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">group<span class="idiff left">_name</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">group</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">sample_name</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">group_color</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">group_colors</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">group_name</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">group</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">color</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sample_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">group_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">group_</span>color</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Sample</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;">#000000</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#07661fb9d6b06c26141694495c4ad1703ea3de7a"><strong>paleomix/tools/zonkey/parts/nuclear.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">@@ -192,17 +192,10 @@ class BuildFilteredBEDFilesNode(CommandNode):</td>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdmixtureNode</span><span class="p">(</span><span class="n" style="color: #333;">CommandNode</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC195" 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;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="n" style="color: #333;">output_root</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;">samples</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC197" 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;">_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span></span>
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<pre style="margin: 0;">+<span id="LC195" 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;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="n" style="color: #333;">output_root</span><span class="p">,</span> <span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC196" 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;">_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" 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;">_input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_file</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" 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;">_k_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k_groups</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">group_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)"</span> <span class="o" style="font-weight: 600;">%</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;">_k_groups</span><span class="p">,)</span></span>
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<pre style="margin: 0;">-<span id="LC202" 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;">_supervised</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">((</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">group_key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">())</span></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">),</span> <span class="n" style="color: #333;">k_groups</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">output_root</span><span class="p">,</span></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" 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="220" 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">@@ -227,9 +220,7 @@ class AdmixtureNode(CommandNode):</td>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">set_cwd</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="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">16</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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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC231" 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;">_supervised</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--supervised"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--supervised"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_value</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%(TEMP_OUT_FILE_BED)</span><span class="s" style="color: #d14;">s"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_value</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">k_groups</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="253" 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="244" 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">@@ -253,20 +244,16 @@ class AdmixtureNode(CommandNode):</td>
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253
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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254
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">symlink</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">),</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">basename</span><span class="p">))</span></span>
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255
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"></span>
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256
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<pre style="margin: 0;">-<span id="LC256" 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;">_supervised</span><span class="p">:</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">fam_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">swap_ext</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;">_input_file</span><span class="p">,</span> <span class="s" style="color: #d14;">".fam"</span><span class="p">)</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">fam_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">swap_ext</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;">_input_file</span><span class="p">,</span> <span class="s" style="color: #d14;">".fam"</span><span class="p">)</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">pop_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">swap_ext</span><span class="p">(</span><span class="n" style="color: #333;">fam_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">pop_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reroot_path</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_filename</span><span class="p">)</span></span>
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258
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">pop_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">swap_ext</span><span class="p">(</span><span class="n" style="color: #333;">fam_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pop"</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">pop_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reroot_path</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="n" style="color: #333;">pop_filename</span><span class="p">)</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fam_filename</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fam_handle</span><span class="p">:</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">pop_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pop_handle</span><span class="p">:</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fam_handle</span><span class="p">:</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)"</span> <span class="o" style="font-weight: 600;">%</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;">_k_groups</span><span class="p">,)</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fam_filename</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fam_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">pop_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pop_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fam_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">group</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;">_samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="p">{})</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">pop_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">group</span><span class="p">,))</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">pop_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</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;">_groups</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">),))</span></span>
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270
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"></span>
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271
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"></span>
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272
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SelectBestAdmixtureNode</span><span class="p">(</span><span class="n" style="color: #333;">Node</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="399" 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="386" 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">@@ -399,6 +386,8 @@ class BuildFreqFilesNode(CommandNode):</td>
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399
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">IN_BIM</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".bim"</span><span class="p">,</span></span>
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400
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">IN_FAM</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fam"</span><span class="p">,</span></span>
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401
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">TEMP_OUT_CLUST</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"samples.clust"</span><span class="p">,</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">TEMP_OUT_IMISS</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".imiss"</span><span class="p">,</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">TEMP_OUT_LMISS</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".lmiss"</span><span class="p">,</span></span>
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402
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">OUT_NOSEX</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".frq.strat.nosex"</span><span class="p">,</span></span>
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403
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">OUT_LOG</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".frq.strat.log"</span><span class="p">,</span></span>
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404
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">TEMP_OUT_PREFIX</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">basename</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="692" 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="681" 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">@@ -692,8 +681,9 @@ class PlotPCANode(CommandNode):</td>
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692
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"></span>
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693
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"></span>
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694
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PlotCoverageNode</span><span class="p">(</span><span class="n" style="color: #333;">CommandNode</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC695" 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;">contigs</span><span class="p">,</span> <span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC684" 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;">contigs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">mapping</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;"> <span id="LC685" 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;">_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contigs</span></span>
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<pre style="margin: 0;">+<span id="LC686" 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;">_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">mapping</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">mapping</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC687" 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;">_input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_file</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python"> <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rtools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rscript</span><span class="p">(</span><span class="s" style="color: #d14;">"zonkey"</span><span class="p">,</span> <span class="s" style="color: #d14;">"coverage.r"</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">@@ -726,19 +716,11 @@ class PlotCoverageNode(CommandNode):</td>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contig_name_to_plink_name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'X'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_contigs</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python"> <span class="n" style="color: #333;">name</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;">_mapping</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_contigs</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Excluding contigs is allowed</span></span>
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">)</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;">_contigs</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'Size'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">NodeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Size mismatch between database and BAM; "</span></span>
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="python"> <span class="s" style="color: #d14;">"expected size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i, found </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i for contig </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r"</span></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">size</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;">_contigs</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'Size'</span><span class="p">],</span></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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741
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="python"></span>
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="python"> <span class="s" style="color: #d14;">'ID'</span><span class="p">:</span> <span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="s" style="color: #d14;">'Size'</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;">_contigs</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'Size'</span><span class="p">],</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#952029038f001015c0d133ad89bf6add98045448"><strong>paleomix/tools/zonkey/parts/report.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" 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">@@ -139,26 +139,19 @@ class ReportNode(Node):</td>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">output_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">_SECTION_HEADER</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"samples"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Reference Panel"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">output_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">_SAMPLE_LIST_HEADER</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">group_headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</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;">_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span><span class="p">):</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">group_headers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" <th>Group(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i)</th>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">k_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">output_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">_SAMPLE_LIST_HEADER</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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;">group_headers</span><span class="p">),))</span></span>
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143
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">last_group_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">last_group_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</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;">_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itervalues</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">row</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(2)"</span><span class="p">],</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(3)"</span><span class="p">],</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">])):</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</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;">_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">()):</span></span>
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151
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_group_2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(2)"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">last_group_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(2)"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">last_group_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(3)"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC155" 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="LC156" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(2)"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_group_3</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(3)"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">last_group_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(3)"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC160" 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="LC161" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Group(3)"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" <td></span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</td>"</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;">_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Groups"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</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;">groups</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>
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163
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">pub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"Publication"</span><span class="p">]</span></span>
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164
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pub</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"http"</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="176" 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">@@ -183,7 +176,7 @@ class ReportNode(Node):</td>
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183
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">overview</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_ADMIXTURE_OVERVIEW</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;">ADMIXTURE</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">admixture_v</span><span class="p">)</span></span>
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184
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">output_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">overview</span><span class="p">)</span></span>
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185
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p"><span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">):</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">groups</span></span><span class="p">):</span></span>
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187
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">summary_incl</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;">_build_admixture_cell</span><span class="p">(</span><span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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188
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">summary_excl</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;">_build_admixture_cell</span><span class="p">(</span><span class="n" style="color: #333;">k_groups</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC182" 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">@@ -372,7 +365,7 @@ class AnalysisReport(object):</td>
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Include files showing proproation of ancestral populations,</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># which are required to build admixture figures in the reports.</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p"><span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">groups</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">input_files</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">admix_root</span><span class="p">,</span></span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i.Q"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">postfix</span><span class="p">,</span></span>
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">k_groups</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">@@ -625,9 +618,8 @@ _OVERVIEW_FOOTER = """</td>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"><span class="n" style="color: #333;">_SAMPLE_LIST_HEADER</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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626
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619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"><span class="s" style="color: #d14;"> <table summary="List of samples in the reference panel."></span></span>
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"><span class="s" style="color: #d14;"> <tr></span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"><span class="s" style="color: #d14;"> <th>Group(2)</th></span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python"><span class="s" style="color: #d14;"> <th>Group(3)</th></span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"><span class="s" style="color: #d14;"> <th>ID</th></span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"><span class="s" style="color: #d14;"> <th>Species</th></span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"><span class="s" style="color: #d14;"> <th>Sex</th></span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"><span class="s" style="color: #d14;"> <th>Sample Name</th></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">@@ -637,9 +629,8 @@ _SAMPLE_LIST_HEADER = """</td>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"><span class="n" style="color: #333;">_SAMPLE_LIST_ROW</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"><span class="s" style="color: #d14;"> <tr></span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="python"><span class="s" style="color: #d14;"> <td>{Group(2)}</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="python"><span class="s" style="color: #d14;"> <td>{Group(3)}</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"><span class="s" style="color: #d14;"> <td>{ID}</td></span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"><span class="s" style="color: #d14;">{Groups}</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"><span class="s" style="color: #d14;"> <td><em>{Species}</em></td></span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"><span class="s" style="color: #d14;"> <td>{Sex}</th></span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"><span class="s" style="color: #d14;"> <td>{SampleID}</td></span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#a4ca0c984f1c357ecc12750d6ee9964c69e69104"><strong>paleomix/tools/zonkey/parts/summary.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">@@ -146,7 +146,7 @@ class SummaryNode(Node):</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">admix_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</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;">_root</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">"results"</span><span class="p">,</span> <span class="s" style="color: #d14;">"admixture"</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p"><span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">groups</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">admix_root</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i.Q"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">postfix</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">k_groups</span><span class="p">))</span></span>
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152
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<pre style="margin: 0;"> <span id="LC152" 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">@@ -189,7 +189,7 @@ class SummaryNode(Node):</td>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">admix_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</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;">_root</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="s" style="color: #d14;">"results"</span><span class="p">,</span> <span class="s" style="color: #d14;">"admixture"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p"><span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">groups</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">admix_root</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i.Q"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">postfix</span><span class="p">,</span> <span class="n" style="color: #333;">k_groups</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" <td>"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/compare/0313756ec7fe5613be8c89f9e6cf25f87cde0459...d494bff3f643877763c516b132b22a2331cc0dc3#bdd39bf22335b3c612da534e11b43abc4f368d2b"><strong>paleomix/tools/zonkey/pipeline.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">@@ -37,6 +37,8 @@ from paleomix.common.console import \</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">print_info</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;">print_warn</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.common.formats.fasta</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FASTA</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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> \</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">Pypeline</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" 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">@@ -122,7 +124,7 @@ def build_admixture_nodes(config, data, root, plink):</td>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">admix_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">root</span><span class="p">,</span> <span class="s" style="color: #d14;">"results"</span><span class="p">,</span> <span class="s" style="color: #d14;">"admixture"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">report_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">root</span><span class="p">,</span> <span class="s" style="color: #d14;">"figures"</span><span class="p">,</span> <span class="s" style="color: #d14;">"admixture"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p"><span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k_groups</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">groups</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">plink</span><span class="p">[</span><span class="s" style="color: #d14;">"root"</span><span class="p">],</span> <span class="n" style="color: #333;">postfix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".bed"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" 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="134" 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">@@ -132,7 +134,7 @@ def build_admixture_nodes(config, data, root, plink):</td>
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132
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nuclear</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AdmixtureNode</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span></span>
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133
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">output_root</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_root</span><span class="p">,</span></span>
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134
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">k_groups</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">k_groups</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">samples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">samples</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">groups</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">groups</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">k_groups</span></span><span class="p"><span class="idiff right">]</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">bed_node</span><span class="p">,))</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">replicates</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;">node</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="230" 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">@@ -228,10 +230,11 @@ def build_pca_nodes(config, data, root, plink):</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nodes</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_coverage_nodes</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">data</span></span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_coverage_nodes</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">contigs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mapping</span></span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">()):</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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;">root</span><span class="p">,</span> <span class="s" style="color: #d14;">'figures'</span><span class="p">,</span> <span class="s" style="color: #d14;">'coverage'</span><span class="p">,</span> <span class="s" style="color: #d14;">'coverage'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nuclear</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PlotCoverageNode</span><span class="p">(</span><span class="n" style="color: #333;">contigs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nuclear</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PlotCoverageNode</span><span class="p">(</span><span class="n" style="color: #333;">contigs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">contigs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">mapping</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mapping</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">input_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nuc_bam</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">output_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_prefix</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dependencies</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" 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">@@ -278,6 +281,8 @@ def build_pipeline(config, root, nuc_bam, mito_bam, cache):</td>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sample_tbl</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nuc_bam</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">nuc_bam</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_bam_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nuc_bam</span><span class="p">[</span><span class="s" style="color: #d14;">"Path"</span><span class="p">],</span> <span class="n" style="color: #333;">nuc_bam</span><span class="p">[</span><span class="s" style="color: #d14;">"Info"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># When not sampling, BuildTPED relies on indexed access to ease</span></span>
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># processing of one chromosome at a time. The index is further required</span></span>
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for idxstats used by the PlotCoverageNode.</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">@@ -292,8 +297,11 @@ def build_pipeline(config, root, nuc_bam, mito_bam, cache):</td>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">plink</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">admixture_only</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">build_coverage_nodes</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="p">,</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">nuc_bam</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,)))</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">build_coverage_nodes</span><span class="p">(</span><span class="n" style="color: #333;">contigs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">mapping</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nuc_bam_info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nuclear_contigs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">root</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">nuc_bam</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nuc_bam</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,)))</span></span>
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">build_pca_nodes</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">plink</span><span class="p">))</span></span>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">build_treemix_nodes</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="392" 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">@@ -384,8 +392,6 @@ def setup_mito_mapping(config):</td>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"></span>
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393
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<pre style="margin: 0;"> <span id="LC393" 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;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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386
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">mkfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" # Group: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Group(3)'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NA'</span><span class="p">),))</span></span>
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389
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">mkfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" # Species: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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390
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NA'</span><span class="p">),))</span></span>
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391
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<td class="diff-line-num new_line" data-linenumber="397" 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">
397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">mkfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" # Sex: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="401" 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="407" 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">@@ -401,6 +407,11 @@ def setup_mito_mapping(config):</td>
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401
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<td class="diff-line-num new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.fasta"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,))</span></span>
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402
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="403" 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">
403
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<td class="diff-line-num new_line" data-linenumber="409" 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">
409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_fpath</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_handle</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="410" 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">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FASTA</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">meta</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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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"></span>
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404
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">fasta_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">))</span></span>
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405
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">fasta_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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406
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"></span>
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