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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedops">Debian Med / bedops</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/2ab59170364ec6eabea33713c8bc12338182908a">2ab59170</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T06:27:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: s/python/python3/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/ac60215cbe60c4893a0a5b1379ed476d4b116f87">ac60215c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T06:28:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: Trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/18ec6d6656d18da7bf779882ce328ff2ae7e6cac">18ec6d66</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T06:28:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/70a9f9ca9ebab69e0c7ba04829da2fa50e5ada58">70a9f9ca</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T06:28:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/cf9882538ebeb80eb2b282ea0e268b65b96874aa">cf988253</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T07:16:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Close bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/a19b30fcf4499dc1430d34032e85e3d4f1e2b63a">a19b30fc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T07:23:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix shebang lines in Python scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedops/commit/0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2">0ceb0cf9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-11T07:35:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</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/bedops/compare/479c48082baee8724016641cfcbd6194d5d6848e...0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bedops (2.4.37+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Depends: s/python/python3/ + fix shebang lines in Python scripts</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #948590</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit.</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove obsolete field Name from debian/upstream/metadata (already</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"> present in machine-readable debian/copyright).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 11 Jan 2020 07:24:20 +0100</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">bedops (2.4.37+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<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">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +19,7 @@ bedops (2.4.37+dfsg-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 23 Oct 2019 16:44:58 +0200</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">bedops (2.4.36+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> * Use 2to3 to port python files from python2 to python3</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Closes: #936197</span>
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<a href="https://salsa.debian.org/med-team/bedops/compare/479c48082baee8724016641cfcbd6194d5d6848e...0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2#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">@@ -20,7 +20,7 @@ Package: bedops</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> tcsh</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Description: high-performance genomic feature operations</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> BEDOPS is a suite of tools to address common questions raised in genomic</span>
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<a href="https://salsa.debian.org/med-team/bedops/compare/479c48082baee8724016641cfcbd6194d5d6848e...0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</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">@@ -4,10 +4,14 @@ Bug-Debian: https://bugs.debian.org/936197</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-09-13</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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;">--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py</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;">+++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" 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="LC12" class="line" lang="diff"> </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"> # BEDOPS</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> #</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,10 +21,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.p</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-slurm.py</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/applications/bed/sort-bed/src/update-sort-bed-slurm.py</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/applications/bed/sort-bed/src/update-sort-bed-slurm.py</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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="LC28" 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="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> # BEDOPS</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> #</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">@@ -30,10 +38,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> import sys</span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py</span></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;">--- a/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py</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;">+++ b/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" 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="LC45" 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="LC46" class="line" lang="diff"> </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"> # BEDOPS</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> #</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="55" 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">@@ -43,10 +55,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> import sys</span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/applications/bed/starch/src/starch-diff.py</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/applications/bed/starch/src/starch-diff.py</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/applications/bed/starch/src/starch-diff.py</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/applications/bed/starch/src/starch-diff.py</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/applications/bed/starch/src/starch-diff.py</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" 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="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # BEDOPS</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> #</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">@@ -79,10 +95,14 @@ Index: bedops/applications/bed/starch/src/starch-diff.py</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> uncommon_chromosomes.sort()</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> if args.debug: logger.info('Uncommon chromosomes [%s]' % (','.join(uncommon_chromosomes))) </span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> import os, sys, subprocess</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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86
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"><span class="p">@@ -10,35 +10,35 @@</span> chr1_proc = subprocess.Popen([unstarch,</span>
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87
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> chr1_proc_out, chr1_proc_err = chr1_proc.communicate()</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> chr1_proc_out.strip('\n')</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">@@ -124,10 +144,14 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has</td>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> sys.exit(os.EX_USAGE)</span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="diff"> sys.exit(os.EX_OK)</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC150" 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="LC151" 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="LC152" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> import os, sys, subprocess</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"><span class="p">@@ -10,35 +10,35 @@</span> chr1_proc = subprocess.Popen([unstarch,</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"> chr1_proc_out, chr1_proc_err = chr1_proc.communicate()</span>
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133
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="diff"> chr1_proc_out.strip('\n')</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">@@ -169,10 +193,8 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has</td>
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169
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="diff"> sys.exit(os.EX_USAGE)</span>
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170
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="diff"> </span>
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171
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="diff"> sys.exit(os.EX_OK)</span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bedops/docs/conf.py</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bedops.orig/docs/conf.py</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bedops/docs/conf.py</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/conf.py</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/conf.py</span></span>
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176
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="diff"><span class="p">@@ -42,8 +42,8 @@</span> source_suffix = '.rst'</span>
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177
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="diff"> master_doc = 'index'</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="diff"> </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">@@ -232,3 +254,38 @@ Index: bedops/docs/conf.py</td>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="diff"> # The language of the text. It defaults to the language option</span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="diff"> # or en if the language is not set.</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/applications/bed/starch/test/unsortable_elements/src/isUnsortable.py</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/applications/bed/starch/test/unsortable_elements/src/isUnsortable.py</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> import os, sys, subprocess</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> </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 class="gd" style="color: #000; background-color: #fdd;">--- a/tests/starch/generate_random_intervals.sh</span></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"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/starch/generate_random_intervals.sh</span></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="p">@@ -6,7 +6,7 @@</span> maxLength=$3</span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> # rand=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && rand=$(($rand % 1234))</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"> # rand=$(shuf -i 0-${upperBound} -n ${samples})</span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# rand=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${upperBound})))")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# rand=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${upperBound})))")</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> </span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> while IFS='' read -r line || [[ -n "$line" ]]; do</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"> chr=`printf "$line" | awk '{ print $1 }'`</span>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="p">@@ -18,10 +18,10 @@</span> while IFS='' read -r line || [[ -n "$lin</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"> # length=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && length=$(($length % $maxLength))</span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> # start=$(shuf -i 0-${adjustedBound} -n 1)</span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> # length=$(shuf -i 0-${maxLength} -n 1)</span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # start=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${adjustedBound})))")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # length=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${maxLength})))")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # start=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${adjustedBound})))")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # length=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${maxLength})))")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> # stop=$(($start + $length + 1))</span>
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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> # echo -e "$chr\t$start\t$stop\tid-$chrN-$sample"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(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="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"><span class="gd" style="color: #000; background-color: #fdd;">- echo $(python -S -c "import sys; import random; start=random.randrange(0,${adjustedBound}); length=random.randrange(0,${maxLength}); stop=start+length+1; sys.stdout.write('${chr}\t%s\t%s\tid-${chrN}-${sample}\n' % (start, stop))") | tr " " "\t"</span></span>
</pre>
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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"><span class="gi" style="color: #000; background-color: #dfd;">+ echo $(python3 -S -c "import sys; import random; start=random.randrange(0,${adjustedBound}); length=random.randrange(0,${maxLength}); stop=start+length+1; sys.stdout.write('${chr}\t%s\t%s\tid-${chrN}-${sample}\n' % (start, stop))") | tr " " "\t"</span></span>
</pre>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> done</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-done < "${boundsFn}"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+done < "${boundsFn}"</span></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/bedops/compare/479c48082baee8724016641cfcbd6194d5d6848e...0ceb0cf9a00a2502e100f29a23c370f1fe47f4c2#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Cite-As: |</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> BEDOPS: high-performance genomic feature operations</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Bioinformatics (2012) 28 (14): 1919-1920.</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Name: bedops</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> BEDOPS: high-performance genomic feature operations</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Bioinformatics (2012) 28 (14): 1919-1920.</span>
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6
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Reference:</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> - Author: ></span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Shane Neph and M. Scott Kuehn and Alex P. Reynolds and Eric Haugen and</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Robert E. Thurman and Audra K. Johnson and Eric Rynes and</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Matthew T. Maurano and Jeff Vierstra and Sean Thomas and</span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Richard Sandstrom and Richard Humbert and John A. Stamatoyannopoulos</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> Title: "BEDOPS: high-performance genomic feature operations"</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> Publisher: Bioinformatics</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> Year: 2012</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Volume: 28</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> Number: 14</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Pages: 1919-1920</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/bts277</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">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> PMID: 22576172</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> eprint: "https://academic.oup.com/bioinformatics/article-pdf/\</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> 28/14/1919/582641/bts277.pdf"</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Author: ></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Shane Neph and M. Scott Kuehn and Alex P. Reynolds and Eric Haugen and</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Robert E. Thurman and Audra K. Johnson and Eric Rynes and</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Matthew T. Maurano and Jeff Vierstra and Sean Thomas and</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Richard Sandstrom and Richard Humbert and John A. Stamatoyannopoulos</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Title: 'BEDOPS: high-performance genomic feature operations'</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Publisher: Bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Year: 2012</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Volume: 28</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Number: 14</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Pages: 1919-1920</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/bts277</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> PMID: 22576172</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> eprint: https://academic.oup.com/bioinformatics/article-pdf/28/14/1919/582641/bts277.pdf</span>
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23
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> - Name: bio.tools</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> Entry: Bedops</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> - Name: OMICtools</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> Entry: OMICS_00949</span>
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<td class="diff-line-num old old_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> - Name: SciCrunch</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> Entry: SCR_012865</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> Entry: bedops</span></pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- Name: bio.tools</span>
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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Entry: Bedops</span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Entry: OMICS_00949</span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Entry: SCR_012865</span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="plaintext"> Entry: bedops</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Bug-Database: https://github.com/bedops/bedops/issues</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Bug-Submit: https://github.com/bedops/bedops/issues/new</span></pre>
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