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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbalign">Debian Med / pbalign</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/f12bd4e00e3ba13a459b25b72abcfbef57cce225">f12bd4e0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:00:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself as Uploader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/8ff56925965ec8bfb3931b42016d57b6ed136267">8ff56925</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:02:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port from Python2 to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/a83c7c4dbaa738bfbd7ee7c50633588521f1ae2e">a83c7c4d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:02:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/179cd3639e4c6c3aaed045ceb6d9d1212cbf2b70">179cd363</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:03:03Z</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/pbalign/commit/8c2378cd4b8b8fbef78148ab1e39b3754fed4557">8c2378cd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:03:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: Trailing whitespace in debian/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/517498f61717f23627fe7ea6497285e1775455a6">517498f6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:03:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/8cd30c0de9ffd1ff53f5f08744d5d87a7ed1aeb6">8cd30c0d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:03:09Z</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/pbalign/commit/e87bb50fa5291f97ca1b40889052cbaba6d3fcae">e87bb50f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:12:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Python3 in packaging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbalign/commit/fdbf75c3577ed02122704966069f19edd7eceb1c">fdbf75c3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:18:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add TODO
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
<span class="deleted-file">
−
debian/README.Debian
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e5946243679b89c6745c4bba06f3d9fdc40d293a">
debian/pbalign.docs
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong>
deleted
</a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pbalign</span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC2" class="line" lang="plaintext">=======</span>
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC4" class="line" lang="plaintext">Some good soul needs to add a Python3 package.</span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">pbalign (0.3.2-2) UNRELEASED; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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"> * Afif removed himself as Uploader</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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add myself as Uploader</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"> * Use 2to3 to port from Python2 to Python3</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"> Closes: #937252</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"> * debhelper-compat 12</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="plaintext"> * Standards-Version: 4.4.1</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"> * Remove trailing whitespace in debian/rules</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Trim trailing whitespace.</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="plaintext"> * Set upstream metadata fields: Repository, Repository-Browse.</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="plaintext"> TODO:</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="plaintext"> - Sphinx has import failures</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> - python3-pbh5tools not yet available</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 13 Dec 2019 10:59:33 +0100</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">pbalign (0.3.2-1) unstable; urgency=medium</span>
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2
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19
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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"> * Team upload</span>
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<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: pbalign</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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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC6" 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<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">-all</span>,</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-setuptools,</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python-pbcore,</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python-pbcommand,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-setuptools,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pbcore,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pbcommand,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-sphinx,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> python-nose</span>
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14
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<pre style="margin: 0;">-<span id="LC14" 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="LC14" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-nose</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pbalign</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pbalign.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/pbalign</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" 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">@@ -19,11 +20,11 @@ Homepage: https://github.com/PacificBiosciences/pbalign</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: pbalign</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python-pbalign (= ${source:Version}),</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> python-pkg-resources,</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> blasr<span class="idiff left right"> (>= 5.3+0)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">Recommends: python-pbh5tools,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pbalign (= ${source:Version}),</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pkg-resources,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> blasr</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Recommends: python<span class="idiff left right">3</span>-pbh5tools,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> hdf5-tools</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Suggests: bowtie2,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> gmap,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="37" 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">@@ -36,12 +37,12 @@ Description: map Pacific Biosciences reads to reference DNA sequences</td>
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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"> This package is part of the SMRTAnalysis suite.</span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">Package: python-pbalign</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Package: python<span class="idiff left right">3</span>-pbalign</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> blasr<span class="idiff left right"> (>= 5.3+0)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">Recommends: python-pbh5tools,</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> blasr</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Recommends: python<span class="idiff left right">3</span>-pbh5tools,</span>
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45
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> hdf5-tools</span>
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46
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Suggests: bowtie2,</span>
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47
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> gmap,</span>
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</li>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port from Python2 to Python3</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/937252</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 13 Dec 2019 10:59:33 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -3,25 +3,25 @@</span> SHELL = /bin/bash -e</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> all: build install</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> build:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py build --executable="/usr/bin/env python"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py build --executable="/usr/bin/python3"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> bdist:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py build --executable="/usr/bin/env python"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py bdist --formats=egg</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py build --executable="/usr/bin/python3"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py bdist --formats=egg</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> install:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> develop:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py develop</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py develop</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> pylint:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pylint --errors-only pbalign</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pylint3 --errors-only pbalign</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> test: pylint</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> # Unit tests</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #find tests/unit -name "*.py" | xargs nosetests</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py test</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py test</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> # End-to-end tests</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> @echo pbalign cram tests require blasr installed.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> find tests/cram -name "*.t" | xargs cram </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span> test: pylint</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> h5test:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> # Tests for pre-3.0 smrtanalysis when default file formats are *.h5</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> @echo pbalign h5 tests require blasr, samtoh5, loadPulses, samFilter and etc installed.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nosetests --verbose tests/unit_h5/*.py</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nosetests3 --verbose tests/unit_h5/*.py</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> find tests/cram_h5 -name "*.t" | xargs cram -v</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> doc:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -40,8 +40,8 @@</span> source_suffix = '.rst'</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> master_doc = 'index'</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> # General information about the project.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-project = u'pbalign'</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-copyright = u'2013, 2013, pbiDevNet'</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project = 'pbalign'</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+copyright = '2013, 2013, pbiDevNet'</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> # The version info for the project you're documenting, acts as replacement for</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> # |version| and |release|, also used in various other places throughout the</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -183,8 +183,8 @@</span> latex_elements = {</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> # Grouping the document tree into LaTeX files. List of tuples</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # (source start file, target name, title, author, documentclass [howto/manual]).</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> latex_documents = [</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'pbalign.tex', u'pbalign Documentation',</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- u'2013, pbiDevNet', 'manual'),</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'pbalign.tex', 'pbalign Documentation',</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '2013, pbiDevNet', 'manual'),</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> ]</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> # The name of an image file (relative to this directory) to place at the top of</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -213,8 +213,8 @@</span> latex_documents = [</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> # One entry per manual page. List of tuples</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> # (source start file, name, description, authors, manual section).</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> man_pages = [</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'pbalign', u'pbalign Documentation',</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [u'2013, pbiDevNet'], 1)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'pbalign', 'pbalign Documentation',</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ['2013, pbiDevNet'], 1)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> ]</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> # If true, show URL addresses after external links.</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -227,8 +227,8 @@</span> man_pages = [</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> # (source start file, target name, title, author,</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> # dir menu entry, description, category)</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> texinfo_documents = [</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'pbalign', u'pbalign Documentation',</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- u'2013, pbiDevNet', 'pbalign', 'One line description of project.',</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'pbalign', 'pbalign Documentation',</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '2013, pbiDevNet', 'pbalign', 'One line description of project.',</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> 'Miscellaneous'),</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> ]</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/__init__.py</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/__init__.py</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> """Initialization."""</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> _changelist = "$Change: 173392 $"</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/alignservice/__init__.py</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/alignservice/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -31,4 +31,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> """Initialization."""</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/alignservice/align.py</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/alignservice/align.py</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> # Author: Yuan Li</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> """This script defines class AlignService."""</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> import logging</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> from copy import copy</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> from pbalign.options import importDefaultOptions</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/alignservice/blasr.py</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/alignservice/blasr.py</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> </span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> # Author: Yuan Li</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> from pbalign.alignservice.align import AlignService</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> from pbalign.utils.fileutil import FILE_FORMATS, real_upath, getFileFormat</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/alignservice/bowtie.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/alignservice/bowtie.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> ###############################################################################</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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="LC168" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> from pbalign.alignservice.fastabasedalign import FastaBasedAlignService</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> from os import path</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> from pbcore.util.Process import backticks</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/alignservice/fastabasedalign.py</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/alignservice/fastabasedalign.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" 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="LC180" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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="LC183" class="line" lang="diff"> ###############################################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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="LC184" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<td class="diff-line-num new new_line" data-linenumber="185" 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="LC185" class="line" lang="diff"> #</span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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="LC186" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span> which converts PacBio reads in BASE/PULS</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> align."""</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> # Author: Yuan Li</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> from pbalign.alignservice.align import AlignService</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> from pbcore.util.Process import backticks</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/alignservice/gmap.py</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/alignservice/gmap.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> ###############################################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> # Author: Yuan Li</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> from os import path</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> from pbalign.alignservice.fastabasedalign import FastaBasedAlignService</span>
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<td class="diff-line-num new new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> from pbalign.utils.fileutil import isExist</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/bampostservice.py</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/bampostservice.py</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import, division, print_function</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> from pbalign.service import Service</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> from pbalign.utils.progutil import Execute</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/ccs.py</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/ccs.py</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span> import pbalign.options</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> class Constants(pbalign.options.Constants):</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> TOOL_ID = "pbalign.tasks.pbalign_ccs"</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DRIVER_EXE = "python -m pbalign.ccs --resolved-tool-contract"</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DRIVER_EXE = "python3 -m pbalign.ccs --resolved-tool-contract"</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> INPUT_FILE_TYPE = FileTypes.DS_CCS</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> OUTPUT_FILE_TYPE = FileTypes.DS_ALIGN_CCS</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> # some modified defaults</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/filterservice.py</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/filterservice.py</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span> in an input SAM file according to filter</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> from pbalign.service import Service</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS, isExist</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/options.py</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/options.py</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> # Author:Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> """This scripts defines functions for parsing PBAlignRunner options."""</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> import argparse</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> from copy import copy</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="p">@@ -509,7 +509,7 @@</span> def importDefaultOptions(parsedOptions,</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> newOptions = copy(parsedOptions)</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> infoMsg = "Importing default options: "</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> optionsDictView = vars(newOptions)</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k, v in additionalDefaults.iteritems():</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, v in additionalDefaults.items():</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> if (k not in optionsDictView) or (optionsDictView[k] is None):</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> infoMsg += "{k}={v}, ".format(k=optionsDictView[k], v=v)</span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> optionsDictView[k] = v</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/pbalignfiles.py</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/pbalignfiles.py</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> """This script defines class PBALignFiles."""</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> </span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> from pbalign.utils.fileutil import checkInputFile, getRealFileFormat, \</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> checkOutputFile, checkReferencePath, checkRegionTableFile, \</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> getFileFormat, FILE_FORMATS</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/pbalignrunner.py</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/pbalignrunner.py</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/service.py</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/service.py</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> """This script defines a virtual class Service."""</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> from pbalign.utils.progutil import Availability, \</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> CheckAvailability, Execute</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/tasks/align_minorvariants.py</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/tasks/align_minorvariants.py</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span> __version__ = "0.1"</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> class Constants(object):</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> TOOL_ID = "pbalign.tasks.align_minorvariants"</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DRIVER_EXE = "python -m pbalign.tasks.align_minorvariants --resolved-tool-contract "</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DRIVER_EXE = "python3 -m pbalign.tasks.align_minorvariants --resolved-tool-contract "</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> def get_parser():</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/tools/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/tools/__init__.py</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -32,5 +32,5 @@</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> # Author: Yuan Li</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> """Migrate pbpy scripts to bioinformatics."""</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> </span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/tools/createChemistryHeader.py</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/tools/createChemistryHeader.py</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> """createChemistryHeader.py gets chemistry triple information for movies in</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> a BLASR-produced SAM file. It writes a new SAM header file that contains the</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> chemisty information. This header can be used with samtools reheader. Most</span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/tools/extractUnmappedSubreads.py</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/tools/extractUnmappedSubreads.py</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="p">@@ -1,10 +1,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> """</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> Starts with the filtered_reads.fa file. Reads in the control.cmp.h5 and</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> reference.cmp.h5, removing any subreads that map. Writes resulting fasta</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> entries to stdout.</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> """</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> </span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> import sys</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> class ExtractRunner(PBToolRunner):</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> subread data structure."""</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> cmpFile = h5py.File(cmpH5FN, 'r')</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> movieInfo = cmpFile["/MovieInfo"]</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- movieDict = dict(zip(movieInfo["ID"], movieInfo["Name"]))</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ movieDict = dict(list(zip(movieInfo["ID"], movieInfo["Name"])))</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> </span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> numAln = cmpFile["/AlnInfo/AlnIndex"].shape[0]</span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> movieIdIdx, holeIdx, startIdx, endIdx = 2, 7, 11, 12</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/tools/loadChemistry.py</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/tools/loadChemistry.py</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> USAGE = \</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> """</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> loadChemistry.py</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="p">@@ -38,7 +38,7 @@</span> def writeTriples(movieInfoGroup, triples</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> sequencingKit = movieInfoGroup.create_dataset("SequencingKit" , shape=shape, dtype=STRING_DTYPE, maxshape=(None,))</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> softwareVersion = movieInfoGroup.create_dataset("SoftwareVersion", shape=shape, dtype=STRING_DTYPE, maxshape=(None,))</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> </span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (movieName, triple) in triplesByMovieName.items():</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (movieName, triple) in list(triplesByMovieName.items()):</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> if movieName in movieNamesInCmpH5:</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> idx = movieNamesInCmpH5.index(movieName)</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> bindingKit[idx] = triple[0]</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/tools/mask_aligned_reads.py</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/tools/mask_aligned_reads.py</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> """Takes in a rgn.fofn and corresponding cmp.h5. Uses the</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> alignments from the cmp.h5 to mask corresponding regions of</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> the rgn.h5s. Writes output to a new rgn.fofn."""</span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span> class AlignedReadsMasker(object):</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> logging.debug("Log Level set to DEBUG")</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> alignedReads = self._extractAlignedReads()</span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nreads = sum([len(v) for v in alignedReads.values()])</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nreads = sum([len(v) for v in list(alignedReads.values())])</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> logging.info("Extracted {r} reads ({m} movies) from {f}".format(</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> r=nreads, m=len(alignedReads), f=self.inCmpFile))</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/utils/RgnH5IO.py</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/utils/RgnH5IO.py</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> """</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> Region table reader and writer.</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> """</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> __all__ = ["RgnH5Reader",</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> "RgnH5Writer"]</span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> import h5py</span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="p">@@ -199,7 +199,7 @@</span> class RgnH5Reader(object):</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> movieNameString = movieNameAttr</span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not isinstance(movieNameString, basestring):</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not isinstance(movieNameString, str):</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> raise TypeError("Unsupported movieName {m} of type {t}."</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> .format(m=movieNameString,</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> t=type(movieNameString)))</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/utils/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/utils/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> #</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="p">@@ -31,4 +31,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/utils/fileutil.py</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/utils/fileutil.py</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> """This scripts defines functions for handling input and output files."""</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> import os.path as op</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/utils/progutil.py</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/utils/progutil.py</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> </span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> # Author: Yuan Li</span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> from pbcore.util.Process import backticks</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> import logging</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbalign/utils/tempfileutil.py</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbalign/utils/tempfileutil.py</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> ###############################################################################</span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> #</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> from setuptools import setup, find_packages</span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_fileutil.py</span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/test_fileutil.py</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> """Test pbalign.util/fileutil.py"""</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> import tempfile</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_options.py</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/test_options.py</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> </span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> import tempfile</span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> from argparse import *</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_setpath.py</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/test_setpath.py</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> from os import path</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import ConfigParser</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import configparser</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> </span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> """Define test data path for pbalign."""</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> </span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span> NOSE_CFG = path.join(THIS_DIR, "nose.cfg</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> def _get_data_std_dir():</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> """Get the data directory which contains all the unittests files.</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> """</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nosecfg = ConfigParser.SafeConfigParser()</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nosecfg = configparser.SafeConfigParser()</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> nosecfg.readfp(open(NOSE_CFG), 'r')</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> if nosecfg.has_section('data'):</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> data_dir = path.abspath(nosecfg.get('data', 'dataDir'))</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_tool_contract.py</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/test_tool_contract.py</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span> class TestPbalign(pbcommand.testkit.PbTe</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> </span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> class TestPbalignCCS(pbcommand.testkit.PbTestApp):</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DRIVER_BASE = "python -m pbalign.ccs"</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DRIVER_BASE = "python3 -m pbalign.ccs"</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> INPUT_FILES = [</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> pbtestdata.get_file("rsii-ccs"),</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> pbtestdata.get_file("lambdaNEB")</span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="p">@@ -47,7 +47,7 @@</span> class TestPbalignCCS(pbcommand.testkit.P</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> </span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> class TestPbalignMinorVariants(pbcommand.testkit.PbTestApp):</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DRIVER_BASE = "python -m pbalign.tasks.align_minorvariants"</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DRIVER_BASE = "python3 -m pbalign.tasks.align_minorvariants"</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> INPUT_FILES = [</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> pbtestdata.get_file("rsii-ccs"),</span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> pbtestdata.get_file("lambdaNEB")</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit_h5/test_repackservice.py</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit_h5/test_repackservice.py</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> """Test pbalign.forquiverservice.repack."""</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> import unittest</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> from os import path, remove</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> from shutil import copyfile</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit_h5/test_setpath.py</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit_h5/test_setpath.py</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> from os import path</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import ConfigParser</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import configparser</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> </span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> """Define test data path for pbalign."""</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> </span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span> NOSE_CFG = path.join(THIS_DIR, "nose.cfg</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"> def _get_data_std_dir():</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> """Get the data directory which contains all the unittests files.</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nosecfg = ConfigParser.SafeConfigParser()</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nosecfg = configparser.SafeConfigParser()</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> nosecfg.readfp(open(NOSE_CFG), 'r')</span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> if nosecfg.has_section('data'):</span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> data_dir = path.abspath(nosecfg.get('data', 'dataDir'))</span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit_h5/test_sortservice.py</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit_h5/test_sortservice.py</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> """Test pbalign.forquiverservice.sort."""</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> from os import path, remove</span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"> from shutil import copyfile</span></pre>
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<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">find_definitions_from_pbcore.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3.patch</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span></pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/README.Debian</span></pre>
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<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#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">@@ -6,13 +6,13 @@ include /usr/share/dpkg/default.mk</td>
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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">export PYBUILD_NAME = pbalign</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">BUILDDIR = $(CURDIR)/debian/python<span class="idiff left right">-pbalign</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">BUILDDIR = $(CURDIR)/debian/python<span class="idiff left right">3-$(PYBUILD_NAME)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">BINDIR=$(BUILDDIR)/usr/bin</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">HELP2MAN = help2man --no-info --version-string $(DEB_VERSION_UPSTREAM)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">MANDIR = $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1</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">%:</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> dh $@ --with=python<span class="idiff left right">2</span> --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> dh $@ --with=python<span class="idiff left right">3</span> --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_auto_build</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># (which are large) are not provided in the source distribution</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"># export PYTHONPATH=$(CURDIR); \</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"># cd tests/unit && python -m unittest discover</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># cd tests/unit && python<span class="idiff left right">3</span> -m unittest discover</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> dh_install</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">@@ -40,7 +40,7 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> mv $(BINDIR)/* $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">no_override_dh_installmanpages: SHELL=bash</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">no_override_dh_installmanpages:<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">no_override_dh_installmanpages:</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> # Create manpages - this is deactivated in favour of debian/createmanpages script which is executed before creating the package</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> mkdir -p $(MANDIR)</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> declare -A description; \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +52,7 @@ no_override_dh_installmanpages:</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> [extractUnmappedSubreads.py]="Extract unmapped subreads from a fasta file" \</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> ); \</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> set -x \</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> export PYTHONPATH=$(BUILDDIR)/usr/lib/python<span class="idiff left right">2</span>.7/dist-packages; \</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> export PYTHONPATH=$(BUILDDIR)/usr/lib/python<span class="idiff left right">3</span>.7/dist-packages; \</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> for executable in $(BUILDDIR)/usr/bin/*; \</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> do \</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> $(HELP2MAN) --name="$${description[`basename $$executable`]}" \</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">@@ -64,4 +64,3 @@ override_dh_auto_clean:</td>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> rm -rf doc/_build/</span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> rm -f doc/pbalign.alignservice.rst doc/pbalign.rst doc/pbalign.tasks.rst doc/pbalign.tools.rst doc/pbalign.utils.rst</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> rm -rf pbalign.egg-info</span></pre>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Registry:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> - Name: OMICtools</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_18565</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> - Name: SciCrunch</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Entry: NA</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> - Name: bio.tools</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Entry: NA</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Entry: pbalign</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Name: OMICtools</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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_18565</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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Name: SciCrunch</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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Entry: NA</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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Name: bio.tools</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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Entry: NA</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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Entry: pbalign</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Repository: https://github.com/PacificBiosciences/pbalign.git</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Repository-Browse: https://github.com/PacificBiosciences/pbalign</span></pre>
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