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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tnseq-transit">Debian Med / tnseq-transit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/commit/5393164db100874de45ce4f503825be59a3c251e">5393164d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T14:50:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/commit/0f0cdb1f8417c6f5fad9d09e82b23252b96e1056">0f0cdb1f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T14:53:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.3.4'
Update to upstream version '2.3.4'
with Debian dir 73d785446094a7db5206045938456260fa2c4ccd</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/commit/4fb28f5cfeb2f814605f335c4606834382238519">4fb28f5c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T14:53:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/commit/7462ab4957a553db8c7d391d7ca75bfac6999e77">7462ab49</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T14:53:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/commit/98a2d8d534fdb97fd43dac4d3bdab1558e541349">98a2d8d5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T14:54:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/commit/82f48dec3b16d59aeacccc2dd436896cf80a577e">82f48dec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T14:58:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">
src/pytransit/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#00356195138da970d79b40310349b42befe9abe3">
src/pytransit/analysis/hmm.py
</a>
</li>
<li class="file-stats">
<a href="#46073ef784cdc338b0714d64bb6fd29c8fbdaf90">
src/pytransit/analysis/resampling.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># # Mac</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.DS_STORE</span>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.env</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># Byte-compiled / optimized / DLL files</span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">__pycache__/</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">*.py[cod]</span>
</pre>
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<br>
</li>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change log</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">All notable changes to this project will be documented in this file.</span>
</pre>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 2.3.4 2019-01-14</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">-</span> TRANSIT: </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> Minor bug fixes related to flags in Resampling and HMM</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 2.3.3 2018-12-06</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">-</span> TRANSIT: </span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p"> -</span> Minor bug fixes related to flags in HMM</span>
</pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># TRANSIT 2.3.<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># TRANSIT 2.3.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/mad-lab/transit.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/mad-lab/transit) <span class="p">[</span><span class="nv" style="color: teal;">![Documentation Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/projects/transit/badge/?version=latest</span><span class="p">)</span>](http://transit.readthedocs.io/en/latest/?badge=latest) </span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tnseq-transit (2.3.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper 12</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 30 Jan 2019 15:54:42 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">tnseq-transit (2.3.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1</span>~),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">2</span>~),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python-setuptools,</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">@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python-matplotlib,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python-statsmodels,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> bwa</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: http://saclab.tamu.edu/essentiality/transit/</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong>src/pytransit/__init__.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">@@ -2,6 +2,6 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"transit_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tnseq_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"norm_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stat_tools"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" 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;">"v2.3.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC5" 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;">"v2.3.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[TRANSIT]"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#00356195138da970d79b40310349b42befe9abe3"><strong>src/pytransit/analysis/hmm.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">@@ -226,6 +226,7 @@ class HMMMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hmmNormChoice</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetString</span><span class="p">(</span><span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hmmNormChoice</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetCurrentSelection</span><span class="p">())</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;">LOESS</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="LC229" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hmmLoessCheck</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetValue</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="c1" style="color: #998; font-style: italic;">#Get output path</span></span>
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<pre style="margin: 0;"> <span id="LC232" 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;">transit_tools</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;">ctrldata</span><span class="p">[</span><span class="mi" style="color: #099;">0</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">@@ -377,6 +378,8 @@ class HMMMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC378" 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;">output</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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378
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379
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<pre style="margin: 0;"> <span id="LC379" 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;">output</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;">"# Mean:</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%2.2</span><span class="s" style="color: #d14;">f</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;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">average</span><span class="p">(</span><span class="n" style="color: #333;">reads_nz</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC380" 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;">output</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;">"# Median:</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%2.2</span><span class="s" style="color: #d14;">f</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;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">reads_nz</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC381" 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;">output</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;">"# Normalization:</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normalization</span><span class="p">)</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" 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;">output</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;">"# LOESS Correction:</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="nb" style="color: #0086b3;">str</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;">LOESS</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC383" 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;">output</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;">"# pins (obs):</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f</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;">pins_obs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC384" 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;">output</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;">"# pins (est):</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f</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;">pins</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC385" 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;">output</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;">"# Run length (r):</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</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;">r</span><span class="p">)</span></span>
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<li id="46073ef784cdc338b0714d64bb6fd29c8fbdaf90">
<a href="https://salsa.debian.org/med-team/tnseq-transit/compare/5a1ca0994808bbeb565d764dd3b885b70739ba1e...82f48dec3b16d59aeacccc2dd436896cf80a577e#46073ef784cdc338b0714d64bb6fd29c8fbdaf90"><strong>src/pytransit/analysis/resampling.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">@@ -219,6 +219,7 @@ class ResamplingMethod(base.DualConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DualConditionMethod</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 class="n" style="color: #333;">short_name</span><span class="p">,</span> <span class="n" style="color: #333;">long_name</span><span class="p">,</span> <span class="n" style="color: #333;">short_desc</span><span class="p">,</span> <span class="n" style="color: #333;">long_desc</span><span class="p">,</span> <span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="n" style="color: #333;">expdata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">replicates</span><span class="p">,</span> <span class="n" style="color: #333;">LOESS</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">LOESS</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wxobj</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Z</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="LC223" 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="LC224" 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;">adaptive</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adaptive</span></span>
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<pre style="margin: 0;"> <span id="LC225" 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;">doHistogram</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">doHistogram</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" 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">@@ -316,7 +317,6 @@ class ResamplingMethod(base.DualConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">includeZeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">excludeZeros</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">pseudocount</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</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;">"pc"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC319" 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;">Z</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="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Z"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</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;">Z</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="LC321" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</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;">"l"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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