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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tophat">Debian Med / tophat</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tophat/commit/536bdf52e050734d6acfa218cc4223a1dd0e2e02">536bdf52</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T07:58:38Z</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/tophat/commit/acc496f8e406980efb5fe478bb82555cc05cc8fc">acc496f8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:09Z</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/tophat/commit/cb0a23d8f04fa5d2be0a21dce7d4da700ed91d09">cb0a23d8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tophat/commit/3bfee2157f4150e8e5efe810b682f38c6c7a0b04">3bfee215</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:15Z</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/tophat/commit/0115fe4cb8f63176a95224d2367560142b7f0426">0115fe4c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tophat/commit/32d6ceb17704373f6d4a07e2ced979f5aadf02a4">32d6ceb1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Submit.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tophat/commit/621a56187ea3b6825e707603ab64a65dd7e05458">621a5618</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Name, Contact from debian/upstream/metadata.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tophat/commit/69afa00f514be3cdda43c72cf1a0d8b13a3baeec">69afa00f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T08:47:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rely on pre-initialized dpkg-architecture variables.
Fixes lintian: debian-rules-sets-dpkg-architecture-variable
See https://lintian.debian.org/tags/debian-rules-sets-dpkg-architecture-variable.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tophat/commit/f14dd955c6a7246cad81772c5897cd6f73d81d66">f14dd955</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-11T09:08:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More 2to3 stuff, d/control changed from python to python3
</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="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tophat (2.1.1+dfsg1-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #938677</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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove trailing whitespace in debian/control</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Submit.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Remove obsolete fields Name, Contact from debian/upstream/metadata.</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"> * Rely on pre-initialized dpkg-architecture variables.</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> Fri, 11 Oct 2019 09:54:16 +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">tophat (2.1.1+dfsg1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Fix Makefile.am</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">@@ -46,9 +60,9 @@ tophat (2.1.1+dfsg-4) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">tophat (2.1.1+dfsg-3) unstable; urgency=medium</span>
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47
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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"> * Team upload.</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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50
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> [ Nadiya Sitdykova ]</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> * Add autopkgtest test-suite<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> * Add autopkgtest test-suite</span>
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52
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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53
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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54
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> * debhelper 10 (use --no-parallel to avoid build problems)</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,9 +117,9 @@ tophat (2.0.13+dfsg-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> * Adapted patches</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> [ Alexandre Mestiashvili]</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> * debian/patches/hardening4samtols.patch: add hardening flags for<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> * debian/patches/hardening4samtols.patch: add hardening flags for</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"> embedded copy of samtools</span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"> -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Sun, 26 Oct 2014 15:53:02 +0100</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" 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="151" 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">@@ -137,9 +151,9 @@ tophat (2.0.12+dfsg-1) unstable; urgency=medium</td>
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137
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> [ Alexandre Mestiashvili ]</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> * d/watch: new url</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> * Imported Upstream version 2.0.12+dfsg</span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"> resolving #733352.</span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"> removed const_ness_part1.patch as the new patch solves the problem<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> removed const_ness_part1.patch as the new patch solves the problem</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"> completely</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> Closes: #733352</span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"> * debian/patches/fix_includes_path.patch: exclude SeqAn-1.3 from configure.ac</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="167" 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="181" 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">@@ -167,7 +181,7 @@ tophat (2.0.10-1) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">tophat (2.0.9-1) unstable; urgency=low</span>
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<td class="diff-line-num old_line" data-linenumber="168" 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="LC182" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"> * d/get-orig-source: place tarballs to ../tarballs/</span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"> * d/control: use canonical vcs fields, Standards-Version: 3.9.4<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> * d/control: use canonical vcs fields, Standards-Version: 3.9.4</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"> * d/changelog: updated source field</span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"> * refreshed patches</span>
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<td class="diff-line-num old_line" data-linenumber="173" 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="LC187" class="line" lang="plaintext"> * Imported Upstream version 2.0.9</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" 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="218" 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">@@ -204,7 +218,7 @@ tophat (2.0.6-1) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">tophat (2.0.5-1) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"> [ Alexandre Mestiashvili ]</span>
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<td class="diff-line-num old old_line" data-linenumber="207" 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="LC207" class="line" lang="plaintext"> * Imported Upstream version 2.0.5<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> * Imported Upstream version 2.0.5</span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext"> -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de> Fri, 05 Oct 2012 10:56:26 +0200</span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -289,14 +303,14 @@ tophat (1.3.3-1) UNRELEASED; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext"> TODO:</span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext"> * src/SeqAn-1.2 should be excluded</span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="plaintext"> - tophat depends on seqan library which already exists in debian<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> - tophat depends on seqan library which already exists in debian</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"></span>
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294
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext"> [Alexandre Mestiashvili]</span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext"> * New upstream release<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> * New upstream release</span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="plaintext"> * Removed dh-make template from watch file</span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext"> * Added initial copyright data , removed templates , added Source<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> * Added initial copyright data , removed templates , added Source</span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext"> * debian/compat version 8</span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext"> * debian/control<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> * debian/control</span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="plaintext"> - Maintainer: Debian Med Packaging Team</span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="plaintext"> <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="plaintext"> - DM-Upload-Allowed: yes</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -306,9 +320,9 @@ tophat (1.3.3-1) UNRELEASED; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="plaintext"> - added build-dependency quilt</span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="plaintext"> - added seqan-dev as dependency</span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext"> * debian/rules</span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext"> - removed dh-make template<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"> - removed dh-make template</span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext"> * debian/control Added python dependency to binary package</span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="plaintext"> * debian/control Description shouldn't start with package name<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> * debian/control Description shouldn't start with package name</span>
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312
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="plaintext"> * debian/rules removed quilt patch management</span>
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313
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="plaintext"> * Added DEP3 headers to patches.</span>
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314
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext"> * Added Pre-Depends: dpkg (>= 1.15.6) (xz compression) Fixed syntax-error in debian/copyright</span>
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<a href="https://salsa.debian.org/med-team/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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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/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#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">@@ -5,16 +5,16 @@ Uploaders: Carlos Borroto <carlos.borroto@gmail.com>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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8
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<pre style="margin: 0;">+<span id="LC8" 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="LC9" class="line" lang="plaintext"> libbam-dev,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python,</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> seqan-dev<span class="idiff left right"> (>= 1.4)</span>,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> seqan-dev,</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libboost-system-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libboost-thread-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> bowtie</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.0</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tophat</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tophat.git</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: http://ccb.jhu.edu/software/tophat</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,14 +23,14 @@ Package: tophat</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> bowtie2 | bowtie,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> samtools (>= 1.5)</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Suggests: cufflinks</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Description: fast splice junction mapper for RNA-Seq reads</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> high-throughput short read aligner Bowtie, and then analyzes the</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> mapping results to identify splice junctions between exons.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> mapping results to identify splice junctions between exons.</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> TopHat is a collaborative effort between the University of Maryland</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> Center for Bioinformatics and Computational Biology and the</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> University of California, Berkeley Departments of Mathematics and</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/938677</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 11 Oct 2019 09:54:16 +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/src/tophat.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/src/tophat.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -195,11 +195,11 @@</span> GFF_T_VER = 209 #GFF parser version</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"> #mapping types:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-_reads_vs_G, _reads_vs_T, _segs_vs_G, _segs_vs_J = range(1,5)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+_reads_vs_G, _reads_vs_T, _segs_vs_G, _segs_vs_J = list(range(1,5))</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> # execution resuming stages (for now, execution can be resumed only for stages</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> # after the pre-filter and transcriptome searches):</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-_stage_prep, _stage_map_start, _stage_map_segments, _stage_find_juncs, _stage_juncs_db, _stage_map2juncs, _stage_tophat_reports, _stage_alldone = range(1,9)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+_stage_prep, _stage_map_start, _stage_map_segments, _stage_find_juncs, _stage_juncs_db, _stage_map2juncs, _stage_tophat_reports, _stage_alldone = list(range(1,9))</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> stageNames = ["start", "prep_reads", "map_start", "map_segments", "find_juncs", "juncs_db", "map2juncs", "tophat_reports", "alldone"]</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # 0 1 2 3 4 5 6 7 , 8</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> runStages = dict([(stageNames[st], st) for st in range(0, 9)])</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -214,7 +214,7 @@</span> def getResumeStage(rlog):</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> #first line must be the actual tophat command used</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> thcmd=None</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- thcmd = flog.next()</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ thcmd = next(flog)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> except StopIteration:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> die("Error: cannot resume, run.log is empty.")</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> oldargv=thcmd.split()</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -257,7 +257,7 @@</span> def doResume(odir):</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> best_stage = r0stage</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> best_argv = r0argv[:]</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if best_stage == _stage_alldone:</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Nothing to resume."</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Nothing to resume.", file=sys.stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> global resumeStage</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -266,7 +266,7 @@</span> def doResume(odir):</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> def setRunStage(stnum):</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> global currentStage</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, "#>"+stageNames[stnum]+":"</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("#>"+stageNames[stnum]+":", file=run_log)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> currentStage = stnum</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> def init_logger(log_fname):</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -1000,7 +1000,7 @@</span> class TopHatParams:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> "b2-score-min=",</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> "b2-D=",</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> "b2-R="])</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except getopt.error, msg:</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except getopt.error as msg:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> raise Usage(msg)</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> self.splice_constraints.parse_options(opts)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -1023,7 +1023,7 @@</span> class TopHatParams:</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # option processing</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> for option, value in opts:</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if option in ("-v", "--version"):</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "TopHat v%s" % (get_version())</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;">+ print("TopHat v%s" % (get_version()))</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> sys.exit(0)</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> if option in ("-h", "--help"):</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> raise Usage(use_message)</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">@@ -1224,9 +1224,9 @@</span> def th_log(out_str):</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> tophat_logger.info(out_str)</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> def th_logp(out_str=""):</span>
</pre>
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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 >> sys.stderr, out_str</span></span>
</pre>
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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(out_str, file=sys.stderr)</span></span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> if tophat_log:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tophat_log, out_str</span></span>
</pre>
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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"><span class="gi" style="color: #000; background-color: #dfd;">+ print(out_str, file=tophat_log)</span></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>
</pre>
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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"> def die(msg=None):</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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> if msg is not None:</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="85" 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">
85
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -1253,7 +1253,7 @@</span> def prepare_output_dir():</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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> else:</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> try:</span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> os.makedirs(tmp_dir)</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="89" 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">
89
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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="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
</pre>
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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"> die("\nError creating directory %s (%s)" % (tmp_dir, o))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -1287,7 +1287,7 @@</span> def check_bowtie_index(idx_prefix, is_bo</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="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> os.path.exists(idx_rev_1) and \</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="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"> os.path.exists(idx_rev_2):</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="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> if os.path.exists(idx_prefix + ".1.ebwt") and os.path.exists(idx_prefix + ".1.bt2"):</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, bwtbotherr</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(bwtbotherr, file=sys.stderr)</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="100" 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">
100
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> return</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="101" 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">
101
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> else:</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="102" 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">
102
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> if is_bowtie2:</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="103" 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">
103
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -1317,7 +1317,7 @@</span> def check_bowtie_index(idx_prefix, is_bo</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="104" 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">
104
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> os.path.exists(bwtidx_env+idx_rev_1) and \</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="105" 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">
105
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> os.path.exists(bwtidx_env+idx_rev_2):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="106" 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">
106
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> if os.path.exists(bwtidx_env + idx_prefix + ".1.ebwt") and os.path.exists(bwtidx_env + idx_prefix + ".1.bt2"):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, bwtbotherr</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(bwtbotherr, file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> return</span>
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<td class="diff-line-num new new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> die(bwtidxerr)</span>
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<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -1350,7 +1350,7 @@</span> def bowtie_idx_to_fa(idx_prefix, is_bowt</span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> die(fail_str+"Error: bowtie-inspect returned an error\n"+log_tail(logging_dir + "bowtie_inspect_recons.log"))</span>
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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> # Bowtie not found</span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
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;">- except OSError, o:</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="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> die(fail_str+"Error: bowtie-inspect not found on this system. Did you forget to include it in your PATH?")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -1406,7 +1406,7 @@</span> def get_bowtie_version():</span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> while len(bowtie_version)<4:</span>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> bowtie_version.append(0)</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"> return bowtie_version</span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
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;">- except OSError, o:</span></span>
</pre>
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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;">+ except OSError as o:</span></span>
</pre>
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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"> errmsg=fail_str+str(o)+"\n"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> errmsg+="Error: bowtie not found on this system"</span>
</pre>
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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="p">@@ -1471,7 +1471,7 @@</span> def get_index_sam_header(params, idx_pre</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> else:</span>
</pre>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> preamble.append(line)</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> bowtie_sam_header_file, "@HD\tVN:1.0\tSO:coordinate"</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;">+ print("@HD\tVN:1.0\tSO:coordinate", file=bowtie_sam_header_file)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> if read_params.read_group_id and read_params.sample_id:</span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> rg_str = "@RG\tID:%s\tSM:%s" % (read_params.read_group_id,</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> read_params.sample_id)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="p">@@ -1490,20 +1490,20 @@</span> def get_index_sam_header(params, idx_pre</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> if read_params.seq_platform:</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> rg_str += "\tPL:%s" % read_params.seq_platform</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
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;">- print >> bowtie_sam_header_file, rg_str</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="144" 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">
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;">+ print(rg_str, file=bowtie_sam_header_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> </span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> if not params.keep_fasta_order:</span>
</pre>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> sq_dict_lines.sort(lambda x,y: cmp(x[0],y[0]))</span>
</pre>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> for [name, line] in sq_dict_lines:</span>
</pre>
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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;">- print >> bowtie_sam_header_file, line</span></span>
</pre>
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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="gd" style="color: #000; background-color: #fdd;">- print >> bowtie_sam_header_file, "@PG\tID:TopHat\tVN:%s\tCL:%s" % (get_version(), run_cmd)</span></span>
</pre>
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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;">+ print(line, file=bowtie_sam_header_file)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@PG\tID:TopHat\tVN:%s\tCL:%s" % (get_version(), run_cmd), file=bowtie_sam_header_file)</span></span>
</pre>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
</pre>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> bowtie_sam_header_file.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> temp_sam_header_file.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> return bowtie_sam_header_filename</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> errmsg=fail_str+str(o)+"\n"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> errmsg+="Error: bowtie not found on this system"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="p">@@ -1559,7 +1559,7 @@</span> def get_samtools_version():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> samtools_version_arr.append(0)</span>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> return version_match.group(), samtools_version_arr</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> errmsg=fail_str+str(o)+"\n"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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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="LC171" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</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="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"> errmsg+="Error: samtools not found on this system"</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"><span class="p">@@ -1668,7 +1668,7 @@</span> class FastxReader:</span>
</pre>
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</td>
<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"> if seq_len != qstrlen :</span>
</pre>
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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"> raise ValueError("Length mismatch between sequence and quality strings "+ \</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> "for %s (%i vs %i)." % (seqid, seq_len, qstrlen))</span>
</pre>
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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="gd" style="color: #000; background-color: #fdd;">- except ValueError, err:</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"><span class="gi" style="color: #000; background-color: #dfd;">+ except ValueError as err:</span></span>
</pre>
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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"> die("\nError encountered parsing file "+self.fname+":\n "+str(err))</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="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"> #return the record</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="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"> self.numrecords+=1</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 class="p">@@ -1705,7 +1705,7 @@</span> class FastxReader:</span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> if seq_len < 3:</span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> raise ValueError("Read %s too short (%i)." \</span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> % (seqid, seq_len))</span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ValueError, err:</span></span>
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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"><span class="gi" style="color: #000; background-color: #dfd;">+ except ValueError as err:</span></span>
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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"> die("\nError encountered parsing fasta file "+self.fname+"\n "+str(err))</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> #return the record and continue</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> self.numrecords+=1</span>
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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"><span class="p">@@ -1744,7 +1744,7 @@</span> def fa_write(fhandle, seq_id, seq):</span>
</pre>
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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"> """</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> line_len = 60</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> fhandle.write(">" + seq_id + "\n")</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(len(seq) / line_len + 1):</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(seq) / line_len + 1):</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> start = i * line_len</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> #end = (i+1) * line_len if (i+1) * line_len < len(seq) else len(seq)</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> if (i+1) * line_len < len(seq):</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="p">@@ -2085,7 +2085,7 @@</span> def prep_reads(params, l_reads_list, l_q</span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> if not use_bam: shell_cmd += ' >' +kept_reads_filename</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> retcode = None</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> try:</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, shell_cmd</span></span>
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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"><span class="gi" style="color: #000; background-color: #dfd;">+ print(shell_cmd, file=run_log)</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> if do_use_zpacker:</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"> filter_proc = subprocess.Popen(prep_cmd,</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> stdout=subprocess.PIPE,</span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="p">@@ -2108,7 +2108,7 @@</span> def prep_reads(params, l_reads_list, l_q</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> if retcode:</span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> die(fail_str+"Error running 'prep_reads'\n"+log_tail(log_fname))</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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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"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> errmsg=fail_str+str(o)</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> die(errmsg+"\n"+log_tail(log_fname))</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="p">@@ -2197,7 +2197,7 @@</span> def bowtie(params,</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> os.remove(unmapped_reads_fifo)</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> try:</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> os.mkfifo(unmapped_reads_fifo)</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
</pre>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> die(fail_str+"Error at mkfifo("+unmapped_reads_fifo+'). '+str(o))</span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> # Launch Bowtie</span>
</pre>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -2231,7 +2231,7 @@</span> def bowtie(params,</span>
</pre>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> unm_zipcmd=[ params.system_params.zipper ]</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"> unm_zipcmd.extend(params.system_params.zipper_opts)</span>
</pre>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> unm_zipcmd+=['-c']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="231" 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">
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 >> run_log, ' '.join(unm_zipcmd)+' < '+ unmapped_reads_fifo + ' > '+ unmapped_reads_out + ' & '</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(' '.join(unm_zipcmd)+' < '+ unmapped_reads_fifo + ' > '+ unmapped_reads_out + ' & ', file=run_log)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> fifo_pid=os.fork()</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> if fifo_pid==0:</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> def on_sig_exit(sig, func=None):</span>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="p">@@ -2440,7 +2440,7 @@</span> def bowtie(params,</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> bowtie_proc.stdout.close()</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> pipeline_proc = fix_order_proc</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> </span>
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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 >> run_log, shellcmd</span></span>
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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(shellcmd, file=run_log)</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> retcode = None</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> if pipeline_proc:</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> pipeline_proc.communicate()</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="p">@@ -2457,7 +2457,7 @@</span> def bowtie(params,</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> pass</span>
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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"> if retcode:</span>
</pre>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> die(fail_str+"Error running:\n"+shellcmd)</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> die(fail_str+"Error: "+str(o))</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> </span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> # Success</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="p">@@ -2491,7 +2491,7 @@</span> def get_gtf_juncs(gff_annotation):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> gtf_juncs_cmd=[prog_path("gtf_juncs"), gff_annotation]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(gtf_juncs_cmd), " > "+gtf_juncs_out_name</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(gtf_juncs_cmd), " > "+gtf_juncs_out_name, file=run_log)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> retcode = subprocess.call(gtf_juncs_cmd,</span>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> stderr=gtf_juncs_log,</span>
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<td class="diff-line-num new new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> stdout=gtf_juncs_out)</span>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="p">@@ -2503,7 +2503,7 @@</span> def get_gtf_juncs(gff_annotation):</span>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> die(fail_str+"Error: GTF junction extraction failed with err ="+str(retcode))</span>
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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> # cvg_islands not found</span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> errmsg=fail_str+str(o)+"\n"</span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> errmsg+="Error: gtf_juncs not found on this system"</span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="p">@@ -2528,13 +2528,13 @@</span> def build_juncs_bwt_index(is_bowtie2, ex</span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> bowtie_build_cmd += [external_splice_prefix + ".fa",</span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> external_splice_prefix]</span>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> try:</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(bowtie_build_cmd)</span></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"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(bowtie_build_cmd), file=run_log)</span></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"> retcode = subprocess.call(bowtie_build_cmd,</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> stdout=bowtie_build_log)</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> if retcode != 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> die(fail_str+"Error: Splice sequence indexing failed with err ="+ str(retcode))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> errmsg=fail_str+str(o)+"\n"</span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> errmsg+="Error: bowtie-build not found on this system"</span>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="p">@@ -2580,7 +2580,7 @@</span> def build_juncs_index(is_bowtie2,</span>
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<td class="diff-line-num new new_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> fusions_file_list,</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"> reference_fasta]</span>
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<td class="diff-line-num new new_line" data-linenumber="291" 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">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(juncs_db_cmd) + " > " + external_splices_out_name</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" 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">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(juncs_db_cmd) + " > " + external_splices_out_name, file=run_log)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> retcode = subprocess.call(juncs_db_cmd,</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> stderr=juncs_db_log,</span>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> stdout=external_splices_out)</span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="p">@@ -2588,7 +2588,7 @@</span> def build_juncs_index(is_bowtie2,</span>
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<td class="diff-line-num new new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> if retcode != 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> die(fail_str+"Error: Splice sequence retrieval failed with err ="+str(retcode))</span>
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<td class="diff-line-num new new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> # juncs_db not found</span>
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<td class="diff-line-num new new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> errmsg=fail_str+str(o)+"\n"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="305" 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">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> errmsg+="Error: juncs_db not found on this system"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="306" 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">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="p">@@ -2621,14 +2621,14 @@</span> def build_idx_from_fa(is_bowtie2, fasta_</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="307" 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">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> bwt_idx_path]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="308" 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">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> th_log("Building Bowtie index from " + os.path.basename(fasta_fname))</span>
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<td class="diff-line-num new new_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(bowtie_idx_cmd)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(bowtie_idx_cmd), file=run_log)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> retcode = subprocess.call(bowtie_idx_cmd,</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> stdout=open(os.devnull, "w"),</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> stderr=open(os.devnull, "w"))</span>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> if retcode != 0:</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> die(fail_str + "Error: Couldn't build bowtie index with err = "</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> + str(retcode))</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> errmsg=fail_str+str(o)+"\n"</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> errmsg+="Error: bowtie-build not found on this system"</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="p">@@ -2639,7 +2639,7 @@</span> def build_idx_from_fa(is_bowtie2, fasta_</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> # Print out the sam header, embedding the user's specified library properties.</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> # FIXME: also needs SQ dictionary lines</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> def write_sam_header(read_params, sam_file):</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sam_file, "@HD\tVN:1.0\tSO:coordinate"</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@HD\tVN:1.0\tSO:coordinate", file=sam_file)</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> if read_params.read_group_id and read_params.sample_id:</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> rg_str = "@RG\tID:%s\tSM:%s" % (read_params.read_group_id,</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> read_params.sample_id)</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="p">@@ -2658,8 +2658,8 @@</span> def write_sam_header(read_params, sam_fi</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> if read_params.seq_platform:</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> rg_str += "\tPL:%s" % read_params.seq_platform</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> </span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sam_file, rg_str</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sam_file, "@PG\tID:TopHat\tVN:%s\tCL:%s" % (get_version(), run_cmd)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(rg_str, file=sam_file)</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@PG\tID:TopHat\tVN:%s\tCL:%s" % (get_version(), run_cmd), file=sam_file)</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> </span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> # Write final TopHat output, via tophat_reports and wiggles</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> def compile_reports(params, sam_header_filename, ref_fasta, mappings, readfiles, gff_annotation):</span>
</pre>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="p">@@ -2727,7 +2727,7 @@</span> def compile_reports(params, sam_header_f</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> report_cmd.append(right_reads)</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> </span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> try:</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(report_cmd)</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(report_cmd), file=run_log)</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> report_proc=subprocess.call(report_cmd,</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> preexec_fn=subprocess_setup,</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> stderr=report_log)</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="p">@@ -2753,8 +2753,7 @@</span> def compile_reports(params, sam_header_f</span>
</pre>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> bam_parts[i],</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> "-o",</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> sorted_bam_parts[i]]</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(bamsort_cmd)</span></span>
</pre>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(bamsort_cmd), file=run_log)</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> </span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> if i + 1 < num_bam_parts:</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> pid = os.fork()</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="p">@@ -2791,7 +2790,7 @@</span> def compile_reports(params, sam_header_f</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> if params.report_params.convert_bam:</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> bammerge_cmd += ["%s.bam" % accepted_hits]</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> bammerge_cmd += bam_parts</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(bammerge_cmd)</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(bammerge_cmd), file=run_log)</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> subprocess.call(bammerge_cmd,</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> stderr=open(logging_dir + "reports.merge_bam.log", "w"))</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> else: #make .sam</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="p">@@ -2807,7 +2806,7 @@</span> def compile_reports(params, sam_header_f</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> stderr=open(logging_dir + "accepted_hits_bam_to_sam.log", "w"))</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> merge_proc.stdout.close()</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> shellcmd = " ".join(bammerge_cmd) + " | " + " ".join(bam2sam_cmd)</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, shellcmd</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(shellcmd, file=run_log)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> sam_proc.communicate()</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> retcode = sam_proc.returncode</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> if retcode:</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="p">@@ -2820,7 +2819,7 @@</span> def compile_reports(params, sam_header_f</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> #just convert to .sam</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> bam2sam_cmd = [samtools_path, "view", "-h", accepted_hits+".bam"]</span>
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<td class="diff-line-num new new_line" data-linenumber="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> shellcmd = " ".join(bam2sam_cmd) + " > " + accepted_hits + ".sam"</span>
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<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, shellcmd</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(shellcmd, file=run_log)</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> r = subprocess.call(bam2sam_cmd,</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> stdout=open(accepted_hits + ".sam", "w"),</span>
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<td class="diff-line-num new new_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> stderr=open(logging_dir + "accepted_hits_bam_to_sam.log", "w"))</span>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="p">@@ -2828,7 +2827,7 @@</span> def compile_reports(params, sam_header_f</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="390" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> die(fail_str+"Error running: "+shellcmd)</span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> os.remove(accepted_hits+".bam")</span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="393" 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">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> die(fail_str+"Error: "+str(o)+"\n"+log_tail(log_fname))</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> </span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="398" 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">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="p">@@ -2851,7 +2850,7 @@</span> def compile_reports(params, sam_header_f</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> merge_cmd=[prog_path("bam_merge"), "-Q",</span>
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<td class="diff-line-num new new_line" data-linenumber="400" 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">
400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> "--sam-header", sam_header_filename, um_merged]</span>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> merge_cmd += um_parts</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(merge_cmd)</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(merge_cmd), file=run_log)</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> ret = subprocess.call( merge_cmd,</span>
</pre>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> stderr=open(logging_dir + "bam_merge_um.log", "w") )</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> if ret != 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="p">@@ -2859,7 +2858,7 @@</span> def compile_reports(params, sam_header_f</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> for um_part in um_parts:</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> os.remove(um_part)</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> </span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> die(fail_str+"Error: "+str(o)+"\n"+log_tail(log_fname))</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> </span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> return junctions</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="p">@@ -2945,15 +2944,15 @@</span> def split_reads(reads_filename,</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> while seg_num + 1 < len(offsets):</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> f = out_segf[seg_num].file</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> seg_seq = read_seq[last_seq_offset+color_offset:offsets[seg_num + 1]+color_offset]</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> f, "%s|%d:%d:%d" % (read_name,last_seq_offset,seg_num, len(offsets) - 1)</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s|%d:%d:%d" % (read_name,last_seq_offset,seg_num, len(offsets) - 1), file=f)</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> if color:</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> f, "%s%s" % (read_seq_temp[last_seq_offset], seg_seq)</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s%s" % (read_seq_temp[last_seq_offset], seg_seq), file=f)</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> else:</span>
</pre>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> f, seg_seq</span></span>
</pre>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(seg_seq, file=f)</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> if not fasta:</span>
</pre>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> seg_qual = read_qual[last_seq_offset:offsets[seg_num + 1]]</span>
</pre>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> f, "+"</span></span>
</pre>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> f, seg_qual</span></span>
</pre>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("+", file=f)</span></span>
</pre>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(seg_qual, file=f)</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> seg_num += 1</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> last_seq_offset = offsets[seg_num]</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> </span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="p">@@ -3049,7 +3048,7 @@</span> def junctions_from_closures(params,</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> left_maps,</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> right_maps])</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> try:</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, ' '.join(juncs_cmd)</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(' '.join(juncs_cmd), file=run_log)</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> retcode = subprocess.call(juncs_cmd,</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> stderr=juncs_log)</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="p">@@ -3057,7 +3056,7 @@</span> def junctions_from_closures(params,</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> if retcode != 0:</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> die(fail_str+"Error: closure-based junction search failed with err ="+str(retcode))</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> # cvg_islands not found</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> th_logp(fail_str + "Error: closure_juncs not found on this system")</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> die(str(o))</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="p">@@ -3088,8 +3087,8 @@</span> def junctions_from_segments(params,</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> return [juncs_out, insertions_out, deletions_out, fusions_out]</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> th_log("Searching for junctions via segment mapping")</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> if params.coverage_search == True:</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\tCoverage-search algorithm is turned on, making this step very slow"</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\tPlease try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory."</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\tCoverage-search algorithm is turned on, making this step very slow", file=sys.stderr)</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\tPlease try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.", file=sys.stderr)</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> </span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> left_maps = ','.join(left_seg_maps)</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> log_fname = logging_dir + "segment_juncs.log"</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="p">@@ -3111,7 +3110,7 @@</span> def junctions_from_segments(params,</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> right_maps = ','.join(right_seg_maps)</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> segj_cmd.extend([right_reads, right_reads_map, right_maps])</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> try:</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(segj_cmd)</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(segj_cmd), file=run_log)</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> retcode = subprocess.call(segj_cmd,</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> preexec_fn=subprocess_setup,</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> stderr=segj_log)</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="p">@@ -3121,7 +3120,7 @@</span> def junctions_from_segments(params,</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> die(fail_str+"Error: segment-based junction search failed with err ="+str(retcode)+"\n"+log_tail(log_fname))</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> </span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> # cvg_islands not found</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> th_logp(fail_str + "Error: segment_juncs not found on this system")</span>
</pre>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> die(str(o))</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="p">@@ -3191,12 +3190,12 @@</span> def join_mapped_segments(params,</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> align_cmd.append(spliced_seg_maps)</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> </span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> try:</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(align_cmd)</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(align_cmd), file=run_log)</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> ret = subprocess.call(align_cmd,</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> stderr=align_log)</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> if ret:</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> die(fail_str+"Error running 'long_spanning_reads':"+log_tail(log_fname))</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> die(fail_str+"Error: "+str(o))</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> </span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> # This class collects spliced and unspliced alignments for each of the</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="p">@@ -3234,13 +3233,13 @@</span> def m2g_convert_coords(params, sam_heade</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> </span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> try:</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> th_log("Converting " + fbasename + " to genomic coordinates (map2gtf)")</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(m2g_cmd) + " > " + m2g_log</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(m2g_cmd) + " > " + m2g_log, file=run_log)</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> ret = subprocess.call(m2g_cmd,</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> stdout=open(m2g_log, "w"),</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> stderr=open(m2g_err, "w"))</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> if ret != 0:</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> die(fail_str + " Error: map2gtf returned an error")</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> err_msg = fail_str + str(o)</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> die(err_msg + "\n")</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> </span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="p">@@ -3269,17 +3268,17 @@</span> def gtf_to_fasta(params, trans_gtf, geno</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> g2f_err = logging_dir + "g2f.err"</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> </span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> try:</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, " ".join(g2f_cmd)+" > " + g2f_log</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" ".join(g2f_cmd)+" > " + g2f_log, file=run_log)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> ret = subprocess.call(g2f_cmd,</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> stdout = open(g2f_log, "w"),</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> stderr = open(g2f_err, "w"))</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> if ret != 0:</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> die(fail_str + " Error: gtf_to_fasta returned an error.")</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> err_msg = fail_str + str(o)</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> die(err_msg + "\n")</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> fver = open(out_fver, "w", 0)</span>
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<td class="diff-line-num new new_line" data-linenumber="531" 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">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> fver, "%d %d %d" % (GFF_T_VER, os.path.getsize(trans_gtf), os.path.getsize(out_fname))</span></span>
</pre>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%d %d %d" % (GFF_T_VER, os.path.getsize(trans_gtf), os.path.getsize(out_fname)), file=fver)</span></span>
</pre>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> fver.close()</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> return out_fname</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="536" 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">
536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="p">@@ -3391,7 +3390,7 @@</span> def get_preflt_data(params, ri, target_r</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> shell_cmd += ' >' + out_unmapped</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> retcode=0</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> try:</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, shell_cmd</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(shell_cmd, file=run_log)</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> if do_use_zpacker:</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> prep_proc = subprocess.Popen(prep_cmd,</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> stdout=subprocess.PIPE,</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="p">@@ -3414,7 +3413,7 @@</span> def get_preflt_data(params, ri, target_r</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> if retcode:</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> die(fail_str+"Error running 'prep_reads'\n"+log_tail(log_fname))</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> </span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> errmsg=fail_str+str(o)</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> die(errmsg+"\n"+log_tail(log_fname))</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> if not out_bam: um_reads.close()</span>
</pre>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="p">@@ -3809,7 +3808,7 @@</span> def get_version():</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> return "__VERSION__"</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> def mlog(msg):</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[DBGLOG]:"+msg</span></span>
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<td class="diff-line-num new new_line" data-linenumber="559" 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">
559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[DBGLOG]:"+msg, file=sys.stderr)</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> </span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> def test_input_file(filename):</span>
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<td class="diff-line-num new new_line" data-linenumber="562" 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">
562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="563" 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">
563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="p">@@ -3835,7 +3834,7 @@</span> def validate_transcriptome(params):</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> inf.close()</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> dlst = fline.split()</span>
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<td class="diff-line-num new new_line" data-linenumber="566" 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">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> if len(dlst)>2:</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tver, tgff_size, tfa_size = map(lambda f: int(f), dlst)</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tver, tgff_size, tfa_size = [int(f) for f in dlst]</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> else:</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> return False</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> tlst=tfa+".tlst"</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="p">@@ -3899,7 +3898,7 @@</span> def main(argv=None):</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> run_log = open(logging_dir + "run.log", "w", 0)</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> global run_cmd</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> run_cmd = " ".join(run_argv)</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, run_cmd</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(run_cmd, file=run_log)</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> </span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> check_bowtie(params)</span>
</pre>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> check_samtools()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="p">@@ -4097,7 +4096,7 @@</span> def main(argv=None):</span>
</pre>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> th_log("A summary of the alignment counts can be found in %salign_summary.txt" % output_dir)</span>
</pre>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> th_log("Run complete: %s elapsed" % formatTD(duration))</span>
</pre>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> </span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Usage, err:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="586" 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">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Usage as err:</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> th_logp(sys.argv[0].split("/")[-1] + ": " + str(err.msg))</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> th_logp(" for detailed help see http://ccb.jhu.edu/software/tophat/manual.shtml")</span>
</pre>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> return 2</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/bed_to_juncs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="591" 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">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/bed_to_juncs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="592" 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">
592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="593" 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">
593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> # encoding: utf-8</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> """</span>
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<td class="diff-line-num new new_line" data-linenumber="597" 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">
597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> bed_to_juncs.py</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="598" 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">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span> def main(argv=None):</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> try:</span>
</pre>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="601" 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">
601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"> opts, args = getopt.getopt(argv[1:], "h", ["help"])</span>
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<td class="diff-line-num new new_line" data-linenumber="602" 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">
602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except getopt.error, msg:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="603" 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">
603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except getopt.error as msg:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="604" 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">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> raise Usage(msg)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="605" 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">
605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="606" 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">
606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> for option, value in opts:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="607" 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">
607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="p">@@ -45,8 +45,8 @@</span> def main(argv=None):</span>
</pre>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> cols = line.split()</span>
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<td class="diff-line-num new new_line" data-linenumber="609" 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">
609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> line_num += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="610" 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">
610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> if len(cols) < 12:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Warning: malformed line %d, missing columns" % line_num</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t", line</span></span>
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<td class="diff-line-num new new_line" data-linenumber="613" 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">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Warning: malformed line %d, missing columns" % line_num, file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="614" 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">
614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t", line, file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="615" 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">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> continue</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> chromosome = cols[0]</span>
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<td class="diff-line-num new new_line" data-linenumber="617" 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">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> orientation = cols[5]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="618" 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">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="p">@@ -56,12 +56,12 @@</span> def main(argv=None):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="619" 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">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> right_pos = int(cols[1]) + block_starts[1]</span>
</pre>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> #print "%s\t%d\t%d\t%s" % (chromosome, left_pos, right_pos, orientation)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="621" 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">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> counts = cols[4]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%s\t%d\t%d\t%s\t%s" % (chromosome, left_pos, right_pos, orientation, counts)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="623" 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">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%d\t%d\t%s\t%s" % (chromosome, left_pos, right_pos, orientation, counts))</span></span>
</pre>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> </span>
</pre>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Usage, err:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="627" 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">
627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t for help use --help"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="629" 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">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Usage as err:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="630" 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">
630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sys.argv[0].split("/")[-1] + ": " + str(err.msg), file=sys.stderr)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="631" 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">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t for help use --help", file=sys.stderr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="632" 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">
632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> return 2</span>
</pre>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"> </span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> </span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/contig_to_chr_coords</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/contig_to_chr_coords</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> # encoding: utf-8</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> """</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> contig_to_chr_coords.py</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span> def main(argv=None):</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"> try:</span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"> try:</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> opts, args = getopt.getopt(argv[1:], "ho:vbg", ["help", "output=", "bed", "gff"])</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except getopt.error, msg:</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except getopt.error as msg:</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"> raise Usage(msg)</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> </span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> arg_is_splice = False</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span> def main(argv=None):</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> arg_is_gff = True</span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> </span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> if (arg_is_splice == False and arg_is_gff == False) or (arg_is_splice == True and arg_is_gff == True):</span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Error: please specify either -b or -g, but not both"</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Error: please specify either -b or -g, but not both", file=sys.stderr)</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> raise Usage(help_message)</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> </span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> if len(args) < 1:</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span> def main(argv=None):</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"> gff_file = open(args[1])</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> </span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> lines = gff_file.readlines()</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print lines[0],</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(lines[0], end=' ')</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"> for line in lines[1:]:</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"> line = line.strip()</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> cols = line.split('\t')</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"><span class="p">@@ -97,7 +97,7 @@</span> def main(argv=None):</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> left_pos = contig[1] + int(cols[3])</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"> right_pos = contig[1] + int(cols[4])</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"> </span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "chr%s\tTopHat\tisland\t%d\t%d\t%s\t.\t.\t%s" % (chr_name, left_pos, right_pos, cols[5],cols[8])</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("chr%s\tTopHat\tisland\t%d\t%d\t%s\t.\t.\t%s" % (chr_name, left_pos, right_pos, cols[5],cols[8]))</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> #print >>sys.stderr, "%s\t%d\t%d\t%s\t%s\t%s\t%s" % (contig[0], left_pos, right_pos,cols[3],cols[6],cols[0],cols[1])</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> </span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"> </span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="p">@@ -105,7 +105,7 @@</span> def main(argv=None):</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> splice_file = open(args[1])</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> </span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> lines = splice_file.readlines()</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print lines[0],</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(lines[0], end=' ')</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> for line in lines[1:]:</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> line = line.strip()</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"> cols = line.split('\t')</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="p">@@ -123,11 +123,11 @@</span> def main(argv=None):</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> left_pos = contig[1] + int(cols[1])</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> right_pos = contig[1] + int(cols[2])</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="692" 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">
692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "chr%s\t%d\t%d\t%s\t0\t%s\t%s\t%s\t255,0,0\t2\t1,1\t%s" % (chr_name, left_pos, right_pos, cols[3],cols[5],left_pos, right_pos,cols[11])</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("chr%s\t%d\t%d\t%s\t0\t%s\t%s\t%s\t255,0,0\t2\t1,1\t%s" % (chr_name, left_pos, right_pos, cols[3],cols[5],left_pos, right_pos,cols[11]))</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> #print >>sys.stderr, "%s\t%d\t%d\t%s\t%s\t%s\t%s" % (contig[0], left_pos, right_pos,cols[3],cols[6],cols[0],cols[1])</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Usage, err:</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t for help use --help"</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Usage as err:</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sys.argv[0].split("/")[-1] + ": " + str(err.msg), file=sys.stderr)</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t for help use --help", file=sys.stderr)</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> return 2</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> </span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> </span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sra_to_solid</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sra_to_solid</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> </span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"> """</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> sra_to_solid.py</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="p">@@ -23,8 +23,8 @@</span> if __name__ == "__main__":</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> if expect_qual % 4 == 3:</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"> line = line[1:]</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"> </span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print line</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(line)</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> expect_qual = (expect_qual + 1) % 4</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"> </span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"> else:</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print use_message;</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(use_message);</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/tophat-fusion-post</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/tophat-fusion-post</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> </span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"> </span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> """</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"><span class="p">@@ -116,12 +116,12 @@</span> class TopHatFusionParams:</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"> "tex-table",</span>
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733
</td>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"> "gtf-file=",</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="734" 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">
734
</td>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> "fusion-pair-dist="])</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="735" 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">
735
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except getopt.error, msg:</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="736" 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">
736
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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="LC736" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except getopt.error as msg:</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="737" 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">
737
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"> raise Usage(msg)</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="738" 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">
738
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="739" 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">
739
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"> for option, value in opts:</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="740" 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">
740
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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="LC740" class="line" lang="diff"> if option in ("-v", "--version"):</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="741" 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">
741
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "TopHat v%s" % (get_version())</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="742" 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">
742
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("TopHat v%s" % (get_version()))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="743" 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">
743
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"> sys.exit(0)</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="744" 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">
744
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"> if option in ("-h", "--help"):</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="745" 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">
745
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"> raise Usage(use_message)</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="746" 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">
746
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="p">@@ -242,7 +242,7 @@</span> def prepare_output_dir():</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="747" 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">
747
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> else:</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="748" 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">
748
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> try:</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="749" 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">
749
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> os.makedirs(tmp_dir)</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="750" 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">
750
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except OSError, o:</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="751" 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">
751
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError as o:</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="752" 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">
752
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"> die("\nError creating directory %s (%s)" % (tmp_dir, o))</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="753" 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">
753
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="754" 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">
754
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="755" 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">
755
</td>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="p">@@ -269,7 +269,7 @@</span> def check_samples():</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="756" 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">
756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> if prev_list != curr_list:</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="757" 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">
757
</td>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> sample_list = open(sample_list_filename, 'w')</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="758" 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">
758
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> for sample in curr_list:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="759" 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">
759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sample_list, sample </span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sample, file=sample_list) </span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"> sample_list.close()</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> return True</span>
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<td class="diff-line-num new new_line" data-linenumber="763" 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">
763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="764" 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">
764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="p">@@ -303,9 +303,9 @@</span> def map_fusion_kmer(bwt_idx_prefix, para</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"> fusion_file.close()</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> </span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> fusion_seq_fa = open(output_dir + "fusion_seq.fa", 'w')</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for seq in seq_dic.keys():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="769" 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">
769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> fusion_seq_fa, ">%s" % seq</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> fusion_seq_fa, seq</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for seq in list(seq_dic.keys()):</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(">%s" % seq, file=fusion_seq_fa)</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(seq, file=fusion_seq_fa)</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> </span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> fusion_seq_fa.close()</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> </span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="p">@@ -322,14 +322,14 @@</span> def map_fusion_kmer(bwt_idx_prefix, para</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> bwtout_file.close()</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"> </span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"> kmer_map = open(fusion_kmer_file_name, 'w')</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for seq, chrs in bwt_dic.items():</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> kmer_map, "%s\t%s" % (seq, ','.join(chrs))</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for seq, chrs in list(bwt_dic.items()):</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%s" % (seq, ','.join(chrs)), file=kmer_map)</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"> </span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"> kmer_map.close()</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"> </span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Extracting 23-mer around fusions and mapping them using Bowtie" % right_now()</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Extracting 23-mer around fusions and mapping them using Bowtie" % right_now(), file=sys.stderr)</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> if sample_update:</span>
</pre>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\tsamples updated"</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\tsamples updated", file=sys.stderr)</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"> </span>
</pre>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"> fusion_kmer_file_name = output_dir + "fusion_seq.map"</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"> </span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="p">@@ -547,7 +547,7 @@</span> def filter_fusion(bwt_idx_prefix, params</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> tmaps.add_map(1, startR, endR, '-', fusion.posR)</span>
</pre>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"> tmaps.add_map(1, startR, endR, '+', fusion.posR)</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"> </span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for m in tmaps.maps.values():</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for m in list(tmaps.maps.values()):</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"> if len(m)==0:</span>
</pre>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"> raise Exception()</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"> </span>
</pre>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"><span class="p">@@ -698,7 +698,7 @@</span> def filter_fusion(bwt_idx_prefix, params</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"> </span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"> return min_value</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"> </span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kmer_len = len(seq_chr_dic.keys()[0])</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ kmer_len = len(list(seq_chr_dic.keys())[0])</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"> sample_name = fusion.split("/")[0][len("tophat_"):]</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"> </span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"> data = os.getcwd().split('/')[-1]</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"><span class="p">@@ -894,7 +894,7 @@</span> def filter_fusion(bwt_idx_prefix, params</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> </span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"> fusion_file.close()</span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Filtering fusions" % right_now()</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Filtering fusions" % right_now(), file=sys.stderr)</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"> </span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> seq_chr_dic = {}</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> seq_chr_file = open(output_dir + "fusion_seq.map", 'r')</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"><span class="p">@@ -976,7 +976,7 @@</span> def filter_fusion(bwt_idx_prefix, params</span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"> juncs_file = file + '/junctions.bed'</span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"> if not os.path.exists(juncs_file):</span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"> juncs_file = None</span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, 'Warning: could not find juctions.bed (%s).' % (juncs_file)</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Warning: could not find juctions.bed (%s).' % (juncs_file), file=sys.stderr)</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"> </span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> ref_file = "refGene.txt"</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"> if not os.path.exists(ref_file):</span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="p">@@ -987,20 +987,20 @@</span> def filter_fusion(bwt_idx_prefix, params</span>
</pre>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"> ens_file = None</span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"> </span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"> if juncs_file is None and ref_file is None and ens_file is None:</span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, 'Warning: neither junctions.bed nor ref/ensGene.txt found.'</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Warning: neither junctions.bed nor ref/ensGene.txt found.', file=sys.stderr)</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"> </span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"> junctions = load_junctions(ref_file, ens_file, juncs_file)</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"> </span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\tProcessing:", fusion_file</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\tProcessing:", fusion_file, file=sys.stderr)</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"> filter_fusion_impl(fusion_file, junctions, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)</span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"> </span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"> fusion_out_file = output_dir + "potential_fusion.txt"</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"> output_file = open(fusion_out_file, 'w')</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> for fusion_gene in fusion_gene_list:</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> for line in fusion_gene:</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> output_file, line</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(line, file=output_file)</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> output_file.close()</span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, '\t%d fusions are output in %s' % (len(fusion_gene_list), fusion_out_file)</span></span>
</pre>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t%d fusions are output in %s' % (len(fusion_gene_list), fusion_out_file), file=sys.stderr)</span></span>
</pre>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"> </span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> </span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> </span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"><span class="p">@@ -1035,7 +1035,7 @@</span> def wait_pids(pids):</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"> </span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"> </span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"> def do_blast(params):</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Blasting 50-mers around fusions" % right_now()</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Blasting 50-mers around fusions" % right_now(), file=sys.stderr)</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"> </span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"> file_name = output_dir + "potential_fusion.txt"</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"> blast_genomic_out = output_dir + "blast_genomic"</span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"><span class="p">@@ -1111,7 +1111,7 @@</span> def do_blast(params):</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"> blast(blast_nt, seq, blast_nt_out)</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"> </span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"> if not os.path.exists(output_dir + "blast_nt/" + seq ):</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t%d. %s" % (count, line[:-1])</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%d. %s" % (count, line[:-1]), file=sys.stderr)</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"> if params.num_threads <= 1:</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"> work()</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"> else:</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"><span class="p">@@ -1437,7 +1437,7 @@</span> def read_dist(params):</span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"> for i in range(len(alignments_list)):</span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"> output_region(sample_name, alignments_list[i], reads_list[i])</span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"> </span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Generating read distributions around fusions" % right_now()</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Generating read distributions around fusions" % right_now(), file=sys.stderr)</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"> </span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"> file_name = output_dir + "potential_fusion.txt"</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"> file = open(file_name, 'r')</span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"><span class="p">@@ -1465,7 +1465,7 @@</span> def read_dist(params):</span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"> </span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"> pids = [0 for i in range(params.num_threads)]</span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"> </span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for sample_name, list in alignments_list.items():</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for sample_name, list in list(alignments_list.items()):</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"> bam_file_name = 'tophat_%s/accepted_hits.bam' % sample_name</span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"> if not os.path.exists(bam_file_name):</span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"> continue</span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"><span class="p">@@ -1473,11 +1473,11 @@</span> def read_dist(params):</span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"> increment = 50</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"> for i in range((len(list) + increment - 1) / increment):</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"> temp_list = list[i*increment:(i+1)*increment]</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, '\t%s (%d-%d)' % (sample_name, i*increment + 1, min((i+1)*increment, len(list)))</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t%s (%d-%d)' % (sample_name, i*increment + 1, min((i+1)*increment, len(list))), file=sys.stderr)</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"> </span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"> alignments_list = []</span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"> for fusion in temp_list:</span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, '\t\t%s' % fusion</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('\t\t%s' % fusion, file=sys.stderr)</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"> fusion = fusion.split()</span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"> alignments_list.append([fusion[0], int(fusion[1]), int(fusion[2]), fusion[3]])</span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"> </span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"><span class="p">@@ -2010,7 +2010,7 @@</span> def generate_html(params):</span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"> num_fusions = 0</span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"> num_alternative_splicing_with_same_fusion = 0</span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="911" 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">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key, value in fusion_dic.items():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="912" 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">
912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key, value in list(fusion_dic.items()):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="913" 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">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"> num_fusions += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="914" 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">
914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"> num_alternative_splicing_with_same_fusion += (value - 1)</span>
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<td class="diff-line-num new new_line" data-linenumber="915" 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">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="916" 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">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"><span class="p">@@ -2215,20 +2215,20 @@</span> def generate_html(params):</span>
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<td class="diff-line-num new new_line" data-linenumber="917" 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">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"> indices_list += c["index"]</span>
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<td class="diff-line-num new new_line" data-linenumber="918" 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">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="919" 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">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"> indices_list = sorted(indices_list)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="920" 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">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\tnum of fusions: %d" % len(cluster_list)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="921" 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">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\tnum of fusions: %d" % len(cluster_list), file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="922" 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">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="923" 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">
923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="diff"> if params.tex_table:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="924" 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">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="diff"> tex_table_file_name = output_dir + 'table.tex'</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="925" 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">
925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="diff"> tex_table_file = open(tex_table_file_name, 'w')</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="926" 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">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'\documentclass{article}'</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="927" 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">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'\usepackage{graphicx}'</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="928" 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">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'\begin{document}'</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="929" 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">
929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'\pagestyle{empty}'</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="930" 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">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r"\center{\scalebox{0.7}{"</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="931" 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">
931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r"\begin{tabular}{| c | c | c | c | c | c | c |}"</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="932" 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">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r"\hline"</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="933" 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">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r"SAMPLE ID & Fusion genes (left-right) & Chromosomes (left-right) & " + \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="934" 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">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r"5$'$ position & 3$'$ position & Spanning reads & Spanning pairs \\"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="935" 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">
935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'\documentclass{article}', file=tex_table_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="936" 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">
936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'\usepackage{graphicx}', file=tex_table_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="937" 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">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'\begin{document}', file=tex_table_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="938" 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">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'\pagestyle{empty}', file=tex_table_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="939" 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">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r"\center{\scalebox{0.7}{", file=tex_table_file)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="940" 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">
940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r"\begin{tabular}{| c | c | c | c | c | c | c |}", file=tex_table_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="941" 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">
941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r"\hline", file=tex_table_file)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="942" 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">
942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r"SAMPLE ID & Fusion genes (left-right) & Chromosomes (left-right) & " + \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="943" 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">
943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ r"5$'$ position & 3$'$ position & Spanning reads & Spanning pairs \\", file=tex_table_file)</span></span>
</pre>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="diff"> </span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="diff"> html_prev.append(r'<HTML>')</span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="diff"> html_prev.append(r'<HEAD>')</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="diff"><span class="p">@@ -2261,7 +2261,7 @@</span> def generate_html(params):</span>
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<td class="diff-line-num new new_line" data-linenumber="948" 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">
948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="diff"> chr1, chr2 = cluster["chr"].split('-')</span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="950" 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">
950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="diff"> if params.tex_table:</span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'\hline'</span></span>
</pre>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'\hline', file=tex_table_file)</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="diff"> </span>
</pre>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="diff"> html_post.append(r'<P><P><P><BR>')</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="955" 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">
955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="diff"> html_post.append(r'%d. %s %s' % (c+1, cluster["chr"], cluster["dir"]))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="956" 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">
956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="diff"><span class="p">@@ -2287,16 +2287,16 @@</span> def generate_html(params):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="957" 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">
957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="958" 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">
958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="diff"> sample_name2 = "testes"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="959" 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">
959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="diff"> </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="960" 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">
960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'%s & %s & %s & %d & %d & %d & %d \\' % \</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="961" 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">
961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'%s & %s & %s & %d & %d & %d & %d \\' % \</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="962" 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">
962
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC962" class="line" lang="diff"> (sample_name2,</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="963" 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">
963
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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="LC963" class="line" lang="diff"> fusion["gene1"] + "-" + fusion["gene2"],</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="964" 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">
964
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC964" class="line" lang="diff"> chr1[3:] + "-" + chr2[3:],</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="965" 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">
965
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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="LC965" class="line" lang="diff"> fusion["left_coord"],</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="966" 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">
966
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC966" class="line" lang="diff"> fusion["right_coord"],</span>
</pre>
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</tr>
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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="967" 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">
967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="diff"> stats[0],</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="968" 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">
968
</td>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stats[1] + stats[2])</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="969" 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">
969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stats[1] + stats[2]), file=tex_table_file)</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="970" 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">
970
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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="LC970" class="line" lang="diff"> </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="971" 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">
971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> txt_file, '%s\t%s\t%s\t%d\t%s\t%s\t%d\t%d\t%d\t%d\t%.2f' % \</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="972" 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">
972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('%s\t%s\t%s\t%d\t%s\t%s\t%d\t%d\t%d\t%d\t%.2f' % \</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="973" 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">
973
</td>
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="diff"> (sample_name,</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="974" 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">
974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="diff"> fusion["gene1"],</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="975" 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">
975
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC975" class="line" lang="diff"> chr1,</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="976" 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">
976
</td>
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="diff"><span class="p">@@ -2307,7 +2307,7 @@</span> def generate_html(params):</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="977" 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">
977
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC977" class="line" lang="diff"> stats[0],</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="978" 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">
978
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC978" class="line" lang="diff"> stats[1],</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="979" 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">
979
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC979" class="line" lang="diff"> stats[2],</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="980" 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">
980
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC980" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fusion["score"])</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="981" 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">
981
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC981" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fusion["score"]), file=txt_file)</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="982" 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">
982
</td>
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="983" 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">
983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="diff"> html_post.append(r'<TR><TD ALIGN="LEFT"><a href="#fusion_%d">%s</a></TD>' % (i, sample_name))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="984" 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">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="diff"> html_post.append(r'<TD ALIGN="LEFT">%s</TD>' % fusion["gene1"])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="985" 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">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="diff"><span class="p">@@ -2534,7 +2534,7 @@</span> def generate_html(params):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="986" 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">
986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="diff"> chr2_exon_list = combine_exon_list(chr2_exon_list)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="987" 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">
987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="988" 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">
988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="diff"> max_intron_length = 100</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="989" 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">
989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def calculate_chr_coord(exon_list, x = sys.maxint):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="990" 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">
990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def calculate_chr_coord(exon_list, x = sys.maxsize):</span></span>
</pre>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="diff"> exon = exon_list[0]</span>
</pre>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="diff"> chr_length = exon[1] - exon[0] + 1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="993" 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">
993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="diff"> if x <= exon[1]:</span>
</pre>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="diff"><span class="p">@@ -2784,19 +2784,19 @@</span> def generate_html(params):</span>
</pre>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="diff"> html_body.append(r'<BODY text="#000000" bgcolor="#FFFFFF" onload="%s">' % fusion_gene_draw_str)</span>
</pre>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="diff"> </span>
</pre>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="diff"> for line in html_prev + javascript + html_body + html_post:</span>
</pre>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> html_file, line</span></span>
</pre>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(line, file=html_file)</span></span>
</pre>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="diff"> </span>
</pre>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="diff"> html_file.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1002" 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">
1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="diff"> txt_file.close()</span>
</pre>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1004" 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">
1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="diff"> if params.tex_table:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1005" 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">
1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r"\hline"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1006" 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">
1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r"\end{tabular}}}"</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="1007" 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">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> tex_table_file, r'\end{document}'</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1008" 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">
1008
</td>
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r"\hline", file=tex_table_file)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1009" 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">
1009
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1009" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r"\end{tabular}}}", file=tex_table_file)</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1010" 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">
1010
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1010" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(r'\end{document}', file=tex_table_file)</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1011" 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">
1011
</td>
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="diff"> tex_table_file.close()</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1012" 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">
1012
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1012" class="line" lang="diff"> os.system("pdflatex --output-directory=%s %s" % (output_dir, tex_table_file_name))</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1013" 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">
1013
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1013" class="line" lang="diff"> </span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1014" 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">
1014
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1014" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Reporting final fusion candidates in html format" % right_now()</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1015" 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">
1015
</td>
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Reporting final fusion candidates in html format" % right_now(), file=sys.stderr)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1016" 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">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1017" 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">
1017
</td>
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="diff"> # Cufflinks-Fusion</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1018" 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">
1018
</td>
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="diff"> fusion_gene_list = []</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1019" 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">
1019
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1019" class="line" lang="diff"><span class="p">@@ -2833,7 +2833,7 @@</span> def tmp_name():</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1020" 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">
1020
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1020" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1021" 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">
1021
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1021" class="line" lang="diff"> def die(msg=None):</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1022" 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">
1022
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1022" class="line" lang="diff"> if msg is not None: </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1023" 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">
1023
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1023" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, msg</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1024" 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">
1024
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1024" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(msg, file=sys.stderr)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1025" 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">
1025
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1025" class="line" lang="diff"> sys.exit(1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1026" 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">
1026
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1026" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1027" 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">
1027
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1027" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1028" 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">
1028
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1028" class="line" lang="diff"><span class="p">@@ -2881,8 +2881,8 @@</span> def main(argv=None):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1029" 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">
1029
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1029" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1030" 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">
1030
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1030" class="line" lang="diff"> bwt_idx_prefix = args[0]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1031" 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">
1031
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1031" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1032" 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">
1032
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1032" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Beginning TopHat-Fusion post-processing run (v%s)" % (right_now(), get_version())</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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</td>
<td class="diff-line-num new new_line" data-linenumber="1033" 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">
1033
</td>
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "-----------------------------------------------" </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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1034" 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">
1034
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1034" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Beginning TopHat-Fusion post-processing run (v%s)" % (right_now(), get_version()), file=sys.stderr)</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1035" 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">
1035
</td>
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-----------------------------------------------", file=sys.stderr) </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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1036" 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">
1036
</td>
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="diff"> </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="1037" 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">
1037
</td>
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="diff"> start_time = datetime.now()</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="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="diff"> prepare_output_dir()</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="1039" 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">
1039
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1039" class="line" lang="diff"><span class="p">@@ -2907,16 +2907,16 @@</span> def main(argv=None):</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="1040" 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">
1040
</td>
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="diff"> run_log = open(logging_dir + "run.log", "w", 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="1041" 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">
1041
</td>
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="diff"> global run_cmd</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1042" 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">
1042
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1042" class="line" lang="diff"> run_cmd = " ".join(argv)</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="1043" 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">
1043
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1043" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> run_log, run_cmd</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1044" 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">
1044
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1044" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(run_cmd, file=run_log)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1045" 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">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="diff"> </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="1046" 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">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="diff"> finish_time = datetime.now()</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1047" 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">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="diff"> duration = finish_time - start_time</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="1048" 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">
1048
</td>
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr,"-----------------------------------------------"</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1049" 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">
1049
</td>
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "[%s] Run complete [%s elapsed]" % (right_now(), formatTD(duration))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1050" 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">
1050
</td>
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-----------------------------------------------", file=sys.stderr)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1051" 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">
1051
</td>
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[%s] Run complete [%s elapsed]" % (right_now(), formatTD(duration)), file=sys.stderr)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1052" 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">
1052
</td>
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1053" 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">
1053
</td>
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except Usage, err:</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1054" 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">
1054
</td>
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1055" 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">
1055
</td>
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\tfor detailed help see http://tophat-fusion.sourceforge.net/manual.html"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1056" 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">
1056
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1056" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Usage as err:</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="1057" 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">
1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sys.argv[0].split("/")[-1] + ": " + str(err.msg), file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1058" 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">
1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\tfor detailed help see http://tophat-fusion.sourceforge.net/manual.html", file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1059" 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">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="diff"> return 2</span>
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<td class="diff-line-num new new_line" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1061" 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">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1062" 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">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/configure.ac</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1063" 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">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.ac</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1064" 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">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> AC_CONFIG_HEADERS([config.h])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1065" 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">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="diff"> # AC_CONFIG_AUX_DIR([build-aux])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1066" 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">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="diff"> AM_INIT_AUTOMAKE</span>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1067" 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">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_ARG_VAR(PYTHON, [python program])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1069" 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">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_ARG_VAR(PYTHON, [python3 program])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1070" 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">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1071" 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">
1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="diff"> # Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.</span>
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<td class="diff-line-num new new_line" data-linenumber="1072" 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">
1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="diff"> CXXFLAGS="$CXXFLAGS"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="diff"><span class="p">@@ -131,6 +131,6 @@</span> echo \</span>
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<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="diff"> "</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="diff"> if test x"${PYTHON}" = x":" || ! test -x "${PYTHON}"; then</span>
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<td class="diff-line-num new new_line" data-linenumber="1077" 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">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "WARNING! python was not found and is required to run tophat"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1078" 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">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo " Please install python and point configure to the installed location"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "WARNING! python3 was not found and is required to run tophat"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo " Please install python3 and point configure to the installed location"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="diff"> fi</span></pre>
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<a href="https://salsa.debian.org/med-team/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -4,3 +4,4 @@ fix-gcc6.patch</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">remove-convenience-copy-of-samtools.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fix-compatibility-with-recent-samtools.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">fix_makefile.am.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">bindir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/bin</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"># according to dpkg-architecture(1) this should be set to support manual invocation</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">include /usr/share/dpkg/architecture.mk</span></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">%:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh $@ --no-parallel</span>
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<a href="https://salsa.debian.org/med-team/tophat/compare/c68101842742c8608b5640e4fad9a0381fdbfde5...f14dd955c6a7246cad81772c5897cd6f73d81d66#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Contact: Cole Trapnell <cole@cs.umd.edu></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Name: TopHat</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> author: Cole Trapnell and Lior Pachter and Steven L. Salzberg</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> title: ></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,13 +10,13 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/btp120</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> PMID: 19289445</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> URL: http://bioinformatics.oxfordjournals.org/content/25/9/1105.short</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> eprint: "http://bioinformatics.oxfordjournals.org/content/\</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> 25/9/1105.full.pdf+html"</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> eprint: "http://bioinformatics.oxfordjournals.org/content/25/9/1105.full.pdf+html"</span>
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17
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> license: Open Access</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
20
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<td class="diff-line-num new_line old" data-linenumber="16" 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="LC20" class="line" lang="plaintext"> Entry: OMICS_01257</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<td class="diff-line-num new_line old" data-linenumber="16" 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="LC21" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> Entry: tophat</span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> - Name: SciCrunch</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> Entry: SCR_013035</span></pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Name: OMICtools</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Entry: OMICS_01257</span>
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<td class="diff-line-num new old_line" data-linenumber="25" 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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: bio.tools</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Entry: tophat</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: SciCrunch</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: SCR_013035</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Bug-Submit: tophat.cufflinks@gmail.com</span></pre>
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