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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/smalt">Debian Med / smalt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/dbd3bcef2830f84b9412b09188c7eaf28c05f8d5">dbd3bcef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:09:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/c893b0ea5419a5e2a65bf905b4c6d3767e580352">c893b0ea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:09:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/0baa95c80b01940e5bd431b7fda6df3867a3d6b1">0baa95c8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:10:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/7f2a2aac3ec727822a50a06aa7472126b5541fbb">7f2a2aac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:10:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/f915116bdd2fcfdd2f5cc331a392ac17322a8d86">f915116b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:10:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/0cc9e7b1a1737a7df2354e1b7ea1a3c09ee41fae">0cc9e7b1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:10:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/f54efbac08c03f4c8143267cfb0504b680a478d9">f54efbac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:10:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Archive, Bug-Submit.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/smalt/commit/2e03054c73b3a523e8fcaebcb94c979f63e01e92">2e03054c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T13:35:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add TODO
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<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="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">smalt (0.7.6-9) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</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"> Closes: #938501</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"> * debhelper-compat 12</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"> * Standards-Version: 4.4.0</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"> * Remove trailing whitespace in debian/changelog</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"> * Use secure URI in debian/watch.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Set upstream metadata fields: Archive, Bug-Submit.</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"> TODO: Fix some Python3 issues in test scripts</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 05 Sep 2019 15:07:37 +0200</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">smalt (0.7.6-8) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * debhelper 11</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="60" 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">@@ -46,7 +60,7 @@ smalt (0.7.6-5) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">smalt (0.7.6-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> * cme fix dpkg-control</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> * Use autotools-dev / since dh-autoreconf does not work this hopefully also<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> * Use autotools-dev / since dh-autoreconf does not work this hopefully also</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> Closes: #765256</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 14 Oct 2014 13:33:15 +0200</span>
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<a href="https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#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/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,15 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbambamc-dev</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/smalt</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/smalt.git</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Homepage: http://www.sanger.ac.uk/science/tools/smalt-0</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Homepage: http<span class="idiff left right">s</span>://www.sanger.ac.uk/science/tools/smalt-0</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: smalt</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: any</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port 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/938501</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: Thu, 05 Sep 2019 15:07:37 +0200</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/misc/SAM.py</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/misc/SAM.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span> class Sam:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> self.tags[tagnam] = (typ, fld)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> self.ok = True</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> else:</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;">- if is_verbose: print "NOT PARSED '%s'" % lin</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;">+ if is_verbose: print("NOT PARSED '%s'" % lin)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> self.blank()</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> def clip(self):</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -106,7 +106,7 @@</span> class Sam:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> return (typ, isCorrect, s, e)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> def strand(self):</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "(%i, %s)" % (self.flag, bool(self.flag & Sam.FLAG_STRAND))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("(%i, %s)" % (self.flag, bool(self.flag & Sam.FLAG_STRAND)))</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> return bool(self.flag & Sam.FLAG_STRAND)</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> def calcUnclippedStart(self):</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -207,7 +207,7 @@</span> class Sam:</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if bool(self.flag & Sam.FLAG_STRAND):</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> (seq, qual, okflg) = self.reverseComplement()</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> if not okflg:</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: when reverse complementing sequence!"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: when reverse complementing sequence!")</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> exit(1)</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> else:</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> seq = self.nt</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -218,7 +218,7 @@</span> class Sam:</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> def asFastq(self, clip=0):</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> namstr, seq, qual = self.asFastqStr()</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> if clip >= len(self.nt):</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: clipped fragment > sequence length\n%s" % (self.qname)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: clipped fragment > sequence length\n%s" % (self.qname))</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> return Sam.FASTQ_FORMAT % (namstr, seq[clip:], qual[clip:])</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> def reverseComplement(self):</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -245,7 +245,7 @@</span> class Sam:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> if not lin: break</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> self.parse(lin, is_verbose)</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> if self.ok: break</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if is_verbose: print "not parsed: %s" % lin</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if is_verbose: print("not parsed: %s" % lin)</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> return not lin # True if EOF</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -259,7 +259,7 @@</span> def fetchNextRead(infil, read):</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> break</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> read.parse(lin)</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> if not read.ok:</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "not parsed: %s" % lin</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("not parsed: %s" % lin)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> continue</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> break</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> #print read.target.varnum()</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="p">@@ -291,8 +291,8 @@</span> def fetchNextPair(infil, samA, samB):</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> errflg = True</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> if errflg:</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: unexpected pair flags.\n%s\n%s\n%s\n%s" % \</span></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;">- (samA.qname, samA.strFlags(), samB.qname, samB.strFlags())</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: unexpected pair flags.\n%s\n%s\n%s\n%s" % \</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;">+ (samA.qname, samA.strFlags(), samB.qname, samB.strFlags()))</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> exit(1)</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"> return (isEOF, switch_flag)</span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -307,7 +307,7 @@</span> def openFile(filnam, mode):</span>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> oufil = open(filnam, mode)</span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> except:</span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR when opening file '%s'" % filnam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR when opening file '%s'" % filnam)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> exit(1)</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> return oufil</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -316,7 +316,7 @@</span> if __name__ == '__main__':</span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> from sys import argv, exit</span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> if len(argv) < 3:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: %s <SAM file (input)> <mapping score threshold>" % argv[0]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: %s <SAM file (input)> <mapping score threshold>" % argv[0])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> exit(1)</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> infilnam = argv[1]</span>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -360,36 +360,36 @@</span> if __name__ == '__main__':</span>
</pre>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> if mnam == old_qnam:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> if read.rname != old_rnam:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> chimictr = chimictr + 1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "[%i, %i]%s: rname1: %s, rname2: %s" % \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (readctr, chimictr, mnam, old_rnam, read.rname)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
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;">+ print("[%i, %i]%s: rname1: %s, rname2: %s" % \</span></span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (readctr, chimictr, mnam, old_rnam, read.rname))</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> else:</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> # a 'proper' pair</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s %i %i %x" % (read.qname, abs(read.isize), read.mapq, int(read.flag))</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s %i %i %x" % (read.qname, abs(read.isize), read.mapq, int(read.flag)))</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> propctr = propctr + 1</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> isizarr.append(abs(read.isize))</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> else:</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> lowqctr = lowqctr + 1</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> if readctr % 100000 == 0:</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%i reads ..." % readctr</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%i reads ..." % readctr)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> pairctr = pairctr/2</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> infil.close()</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%i out of a total of %i reads (%5.2f%%) were mapped." % \</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (readctr - nomapctr, readctr, 100*float(readctr - nomapctr)/readctr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (minqctr, readctr, 100*float(minqctr)/readctr, Sam.MAPQ_NONRANDOM)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%i out of a total of %i reads (%5.2f%%) were mapped." % \</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (readctr - nomapctr, readctr, 100*float(readctr - nomapctr)/readctr))</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (minqctr, readctr, 100*float(minqctr)/readctr, Sam.MAPQ_NONRANDOM))</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> if Sam.MAPQ_NONRANDOM != mapq_min:</span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (highqctr, readctr, 100*float(highqctr)/readctr, mapq_min)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (highqctr, readctr, 100*float(highqctr)/readctr, mapq_min))</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> if pairctr > 0:</span>
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<td class="diff-line-num new new_line" data-linenumber="130" 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">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%i out of a total of %i reads (%5.2f%%) mapped as a proper pair with a mapping score > %i" % \</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (propctr, readctr, 100*float(propctr)/readctr, mapq_min)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%i of %i pairs (%6.3f%%) with a mapping score >= %i mapped to different chromosomes" % \</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (chimictr, pairctr, 200*float(chimictr)/pairctr, mapq_min)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%i out of a total of %i reads (%5.2f%%) mapped as a proper pair with a mapping score > %i" % \</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (propctr, readctr, 100*float(propctr)/readctr, mapq_min))</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%i of %i pairs (%6.3f%%) with a mapping score >= %i mapped to different chromosomes" % \</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (chimictr, pairctr, 200*float(chimictr)/pairctr, mapq_min))</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="139" 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">
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;">- print "There were no reads mapped as pairs."</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;">+ print("There were no reads mapped as pairs.")</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> exit(0)</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/bam_cigar_test.py</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/bam_cigar_test.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="p">@@ -164,19 +164,19 @@</span> def testSAMfilesAreIdentical(filnamA, fi</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> okflg = len(fldA) == len(fldB)</span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> </span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> if not okflg:</span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "lines differ in the number of fields:\n%s\n%s\n" % \</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (linA.strip(), linB.strip())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("lines differ in the number of fields:\n%s\n%s\n" % \</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (linA.strip(), linB.strip()))</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> break</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in SAM_TEST_FIELDS.keys():</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in list(SAM_TEST_FIELDS.keys()):</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> okflg = fldA[i] == fldB[i]</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> if not okflg and i == 0:</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> # samtools-0.1.18 view -h produces non-printing char</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> # directly after header</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> okflg = fldA[i][1:] == fldB[i] or fldA[i] == fldB[i][1:]</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> if not okflg:</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "lines differ in %s:\n%s\n%s\n" % \</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;">- (SAM_TEST_FIELDS[i], linA.strip(), linB.strip())</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;">+ print("lines differ in %s:\n%s\n%s\n" % \</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (SAM_TEST_FIELDS[i], linA.strip(), linB.strip()))</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> break </span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> if not okflg:</span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> break</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/formats.py</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/formats.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="p">@@ -45,9 +45,9 @@</span> class Cigar:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> self.parse(lin)</span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> okflg = self.ok</span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> if Cigar.DEBUG:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "DEBUG:Cigar.next %s" % (okflg)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("DEBUG:Cigar.next %s" % (okflg))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> if Cigar.DEBUG:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "DEBUG:Cigar.next returns %s" % (isEOF)</span></span>
</pre>
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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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("DEBUG:Cigar.next returns %s" % (isEOF))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> return isEOF</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
</pre>
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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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> def parse(self, lin):</span>
</pre>
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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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="p">@@ -66,11 +66,11 @@</span> class Cigar:</span>
</pre>
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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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> self.cigar.strip()</span>
</pre>
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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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> self.ok = True</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> if Cigar.DEBUG:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "DEBUG:Cigar.parse('%s')::'%s'" % (self.lin, self.cigar)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("DEBUG:Cigar.parse('%s')::'%s'" % (self.lin, self.cigar))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> lin.strip()</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> if lin[0] != '#':</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "not parsed: %s" % (lin)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("not parsed: %s" % (lin))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> self._blank()</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> </span>
</pre>
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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"> def getMateNo(self):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="p">@@ -118,10 +118,10 @@</span> def getNextCigarPair(infil, cigA, cigB,</span>
</pre>
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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"> isOk = True</span>
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<td class="diff-line-num new new_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> if not isEOF and mateno_check:</span>
</pre>
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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"> if cigA.qnam[-2] != cigB.qnam[-2]:</span>
</pre>
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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 class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: read names don't match %s, %s" % (cigA.qnam, cigB.qnam)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: read names don't match %s, %s" % (cigA.qnam, cigB.qnam))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> isOk = False</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> elif cigA.getMateNo() != 1 or cigB.getMateNo() != 2:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR in mate number %s [1] and %s [2]" % (cigA.qnam, cigB.qnam)</span></span>
</pre>
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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="gi" style="color: #000; background-color: #dfd;">+ print("ERROR in mate number %s [1] and %s [2]" % (cigA.qnam, cigB.qnam))</span></span>
</pre>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> isOk = False</span>
</pre>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> </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"> return (isOk, isEOF)</span>
</pre>
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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"><span class="p">@@ -151,6 +151,6 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="212" 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">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> infil = openFile(argv[1])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="214" 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">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> while not cig.next(infil):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="215" 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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print cig.qnam</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="216" 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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(cig.qnam)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="217" 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">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="218" 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">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> infil.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="219" 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">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/mthread_test.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="220" 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">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/mthread_test.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="221" 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">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -57,12 +57,12 @@</span> def cmpCigarFiles(cigfilA, cigfilB, is_v</span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> break</span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> if cigA1 != cigB1:</span>
</pre>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> if is_verbose:</span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin)</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin))</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> if cigA1.mapq > MAPQ_THRESH and cigB1.mapq > MAPQ_THRESH:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="228" 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">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> if cigA2 != cigB2:</span>
</pre>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> if is_verbose:</span>
</pre>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin) </span></span>
</pre>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin)) </span></span>
</pre>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> if cigA2.mapq > MAPQ_THRESH and cigB2.mapq > MAPQ_THRESH:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> exit("Discrepancy:\n%s\n%s" % (cigA2.lin, cigB2.lin))</span>
</pre>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> ctr = ctr + 1</span>
</pre>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="p">@@ -93,7 +93,7 @@</span> if __name__ == '__main__':</span>
</pre>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
</pre>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> isOK, pairctr = cmpCigarFiles(oufilnam_ref, oufilnam_thread, VERBOSE)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> if VERBOSE:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="240" 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">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Test ok=%s, number of pairs = %i" % (isOK, pairctr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Test ok=%s, number of pairs = %i" % (isOK, pairctr))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> if not isOK or pairctr != n_pairs_expected:</span>
</pre>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> exit("Using smalt in multi-threaded mode gave inconsistent results!")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> </span>
</pre>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/results_split_test.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/results_split_test.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span> READSEQS = ("@SIM_000000000_contig5121_0</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> "AAAAGAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAA\n"\</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> "+\n"\</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\Ue_^eBfcfcfNfdf^!\n"</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n"</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> )</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> </span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> # cigar:S:16 SIM_000000000_contig5121_000000001_5120_R_20m/1 20 1 - contig5121 1 20 + 20 M 20</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/splitReads_test.py</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/splitReads_test.py</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="p">@@ -79,13 +79,13 @@</span> def checkOutput(cigfilnam, expected_tup)</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> while not cig.next(infil):</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> if linctr > n_tup:</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> allok = False</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: %i cigar lines, expected %i" % \</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (linctr, n_tup)</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: %i cigar lines, expected %i" % \</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (linctr, n_tup))</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> break</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> mateno = cig.getMateNo()</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> observed_tup = (cig.mapcls, mateno, cig.qseg, cig.snam, cig.sseg)</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> if observed_tup not in expected_tup:</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: unexpected tuple: ", observed_tup</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: unexpected tuple: ", observed_tup)</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> allok = False</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> break</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> </span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="p">@@ -94,7 +94,7 @@</span> def checkOutput(cigfilnam, expected_tup)</span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> for i in range(n_tup):</span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> if not okflgs[i]:</span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: could not find tuple: ", expected_tup[i]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: could not find tuple: ", expected_tup[i])</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> allok = False</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> </span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> if not allok:</span>
</pre>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/testdata.py</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/testdata.py</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="p">@@ -139,9 +139,9 @@</span> class DataFiles:</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> for filnam in (self.datafiles + self.tmpfiles):</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> if access(filnam, F_OK):</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> remove(filnam)</span>
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<td class="diff-line-num new new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if is_verbose: print "Removed file '%s'" % filnam</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if is_verbose: print("Removed file '%s'" % filnam)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> else:</span>
</pre>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Could not access file '%s'" % filnam</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Could not access file '%s'" % filnam)</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> self.datafiles = []</span>
</pre>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> self.tmpfiles = []</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> try:</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="p">@@ -159,7 +159,7 @@</span> def openFile(filnam, mode = 'r'):</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> else:</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> oufil = open(filnam, mode)</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> except:</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR when opening file '%s'" % filnam</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR when opening file '%s'" % filnam)</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> exit(1)</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> </span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> return oufil</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">#bam_cigar_test_makefile.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">#try_to_fix_automake.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#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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<td class="diff-line-num new_line old" data-linenumber="2" 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"> Entry: OMICS_00686</span>
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4
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<td class="diff-line-num new_line old" data-linenumber="2" 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"> - Name: SciCrunch</span>
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<td class="diff-line-num old old_line" data-linenumber="5" 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">
5
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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC5" class="line" lang="plaintext"> Entry: SCR_000544</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6" 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">
6
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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Entry: Smalt</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_00686</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: SCR_000544</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Entry: Smalt</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Archive: SourceForge</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Bug-Submit: hp3@sanger.ac.uk</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=3</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">http://sf.net/smalt/smalt-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">http<span class="idiff left right">s</span>://sf.net/smalt/smalt-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></pre>
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