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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/kineticstools">Debian Med / kineticstools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/b3474d5eac4e2956bf22dda0b933278a52cfb55c">b3474d5e</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:02:51+01:00</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/kineticstools/-/commit/cde481528bb724dd09e404cdcb7cdbc33b203226">cde48152</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:02:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.1+git20200729.e3723e0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/206db447aca536f266242074c2c71857b8680a44">206db447</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:03:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.6.1+git20200729.e3723e0+dfsg'
Update to upstream version '0.6.1+git20200729.e3723e0+dfsg'
with Debian dir ef9cde02667253c37aca078c45b264daa427f224</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/695b67a3bfc6ea252c6a07c548cbbbd76240b3d5">695b67a3</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:03:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/d21c7bc0cefb9b19970a73ca3f4295a2cb2c35b7">d21c7bc0</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:03:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/1f625d1cdc11efaab14076c54306be2265c7af60">1f625d1c</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:20:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add myself to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/b55cedef30c65984db9cba78658757127968ad70">b55cedef</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T23:17:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix resources migration to kineticstools-data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/11d7480a363ad9c82d14c63b61ff51f4ecf12812">11d7480a</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T23:32:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">declare kineticstools-data Multi-Arch: foreign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1">e015e687</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-11-25T23:45:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b12f5ac0052d9237edaacf8bc73366288bda6ce3">
kineticsTools/MultiSiteCommon.py
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<li class="file-stats">
<a href="#3de438878d25828a21fc72e3e303cd3d341e4def">
test/test_integration.py
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kineticstools (0.6.1+git20200729.e3723e0+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add myself to Uploaders</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</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="plaintext"> * debhelper-compat 13 (routine-update)</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="plaintext"> * Fix resources migration to data package when several python versions are</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> provided by Debian. (Closes: #973058)</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="plaintext"> * Declare kineticstools-data Multi-Arch: foreign.</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"> -- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 25 Nov 2020 23:45:13 +0100</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">kineticstools (0.6.1+git20200325.3558942+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> [ Etienne Mollier ]</span>
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<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: kineticstools</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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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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3
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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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Étienne Mollier <etienne.mollier@mailoo.org></span>
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4
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<td class="diff-line-num new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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5
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<td class="diff-line-num new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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6
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<td class="diff-line-num new_line old" data-linenumber="7" 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="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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7
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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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num old_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">
8
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all,</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="18" 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">@@ -17,7 +18,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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18
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> python3-pytest-runner <!nocheck>,</span>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python3-pytest-xdist <!nocheck></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kineticstools</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kineticstools.git</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/kineticsTools</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" 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="42" 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">@@ -41,6 +42,7 @@ Description: detection of DNA modifications</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Package: kineticstools-data</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Multi-Arch: foreign</span>
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44
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<td class="diff-line-num new_line" data-linenumber="46" 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="LC46" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<td class="diff-line-num old_line" data-linenumber="45" 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">
45
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Description: detection of DNA modifications -- data files</span>
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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="48" 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="LC48" class="line" lang="plaintext"> Tools for detecting DNA modifications from single molecule, real-time (SMRT®)</span>
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<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -15,6 +15,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">INSTDIR = $(CURDIR)/debian/$(DEB_SOURCE)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">BINDIR = $(INSTDIR)/usr/bin</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">MANDIR = $(INSTDIR)/usr/share/man/</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">DATADIR = $(CURDIR)/debian/kineticstools-data/usr/share/kineticstools/resources</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</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">@@ -26,7 +27,12 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> mkdir -p $(MANDIR)/man1</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> rst2man doc/manual.rst > $(MANDIR)/man1/ipdSummary.1</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> mkdir -p debian/kineticstools-data/usr/share/kineticstools</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> mv debian/python3-kineticstools/usr/lib/python3.*/dist-packages/kineticsTools/resources debian/kineticstools-data/usr/share/kineticstools/</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> # There is probably a simpler way, but that should do for the moment.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> set -e \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> ; for libdir in debian/python3-kineticstools/usr/lib/python3.* \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> ; do rm -rf $(DATADIR) \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> ; mv $${libdir}/dist-packages/kineticsTools/resources $(DATADIR) \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> ; done</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> rm debian/python3-kineticstools/usr/lib/python3.*/dist-packages/nosetests.xml</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<li id="b12f5ac0052d9237edaacf8bc73366288bda6ce3">
<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1#b12f5ac0052d9237edaacf8bc73366288bda6ce3"><strong>kineticsTools/MultiSiteCommon.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">@@ -143,7 +143,7 @@ class MultiSiteCommon(object):</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getContextMeans</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">meanVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</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="LC146" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="p">[(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pre</span><span class="p">):(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)].</span><span class="n" style="color: #333;">tostring</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="p">[(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pre</span><span class="p">):(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)].</span><span class="n" style="color: #333;">tostring</span><span class="p">()<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"ascii"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ctx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">contextMeanTable</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;">meanVector</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">contextMeanTable</span><span class="p">[</span><span class="n" style="color: #333;">ctx</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;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1#3de438878d25828a21fc72e3e303cd3d341e4def"><strong>test/test_integration.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">@@ -13,10 +13,10 @@ EXPECTED_GFF = """\</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6307</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6307</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=56;context=CAGATTAGCACGCTGATGCGCATCAGCGACAAACTGGCGGG;IPDRatio=1.92</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6455</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6455</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">32</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=53;context=CCTGCAAGGACTGGATATGCTGATTCTTATTTCACCTGCGA;IPDRatio=1.78</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6512</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6512</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">32</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=55;context=GTAATCACAACTATCGATCAACTCATTCTCATTTTTTGCTA;IPDRatio=1.81</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m6A</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;identificationQv=5</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;identificationQv=4</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m6A</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;<span class="idiff left right">frac=0.627;fracLow=0.321;fracUp=0.911;</span>identificationQv=5</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;<span class="idiff left right">frac=1.000;fracLow=0.370;fracUp=1.000;</span>identificationQv=4</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20051</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20051</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">44</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=19;context=ACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGT;IPDRatio=2.54</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;identificationQv=9</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;<span class="idiff left right">frac=1.000;fracLow=0.379;fracUp=1.000;</span>identificationQv=9</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20449</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20449</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">31</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=18;context=TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGT;IPDRatio=2.49"""</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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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">@@ -39,6 +39,7 @@ class TestKineticsTools(PbIntegrationBase):</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"--csv"</span><span class="p">,</span> <span class="n" style="color: #333;">csv_out</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"--pvalue"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.001"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"--identify"</span><span class="p">,</span> <span class="s" style="color: #d14;">"m6A,m4C"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"--methylFraction"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"--reference"</span><span class="p">,</span> <span class="n" style="color: #333;">ref_set</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">alignments</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <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">@@ -46,6 +47,7 @@ class TestKineticsTools(PbIntegrationBase):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">gff_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">csv_out</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;">records</span> <span class="o" style="font-weight: 600;">=</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;">print</span><span class="p">(</span><span class="n" style="color: #333;">gff_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">gff_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"rt"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gff</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;">gff</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">splitlines</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC53" 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;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"##"</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -58,4 +60,4 @@ class TestKineticsTools(PbIntegrationBase):</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">csv_records</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</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;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">csv_records</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3222</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">csv_records</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33<span class="idiff left right">,,,</span>'</span></span></pre>
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