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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/harvest-tools">Debian Med / harvest-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/harvest-tools/-/commit/8797c85cb82611a93c931b9b210b63ffdc6a5c6c">8797c85c</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-04-10T10:09:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Python migration using 2to3 tool
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/harvest-tools/-/commit/2b649ab9cefaff102426689adec83de2ed47e157">2b649ab9</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-04-10T10:09:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends python3-setuptools
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/harvest-tools/-/commit/0aae0955a3a2a57c44a5ea13d09e28b9f361cba5">0aae0955</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-04-10T10:22:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/harvest-tools/-/commit/605bed400ccc5fc3823d18f9e269716606fbb013">605bed40</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-04-10T10:26:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/upstream/metadata: Repository and Bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/harvest-tools/-/commit/337cc969d05e07fc117dc82bb4794eb6d591f22b">337cc969</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-04-10T10:26:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#1ceb2d8d4c3058bc1fbb2871ad630215e85070f4">
<span class="new-file">
+
debian/patches/python-2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">harvest-tools (1.3-4.1) 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"> [ Steffen Möller ]</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Non-maintainer upload.</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"> * Added ref to conda.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Antoni Villalonga ]</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"> * Python migration using 2to3 tool.</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"> * Build-Depends python3-setuptools. (Closes: #943055)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.5.0</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"> * d/upstream/metadata: Repository and Bug</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"> -- Antoni Villalonga <antoni@friki.cat> Fri, 10 Apr 2020 10:09:57 +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">harvest-tools (1.3-4) 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"> [ Adrian Bunk ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b#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">@@ -5,13 +5,13 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cython,</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python-setuptools,</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-setuptools,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> protobuf-compiler,</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> capnproto,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libprotobuf-dev,</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libcapnp-dev,</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/harvest-tools</span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/harvest-tools.git</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://harvest.readthedocs.org/en/latest/content/harvest-tools.html</span>
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<li id="1ceb2d8d4c3058bc1fbb2871ad630215e85070f4">
<a href="https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b#1ceb2d8d4c3058bc1fbb2871ad630215e85070f4"><strong>debian/patches/python-2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Antoni Villalonga <antoni@friki.cat></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 10 Apr 2020 10:08:15 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Python migration using 2to3 tool</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/INSTALL.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/INSTALL.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,12 +1,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> import os,sys,string</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #harvest utilities INSTALL script</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> user_home = os.environ["HOME"]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print "<<Welcome to harVest utility script install>>"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("<<Welcome to harVest utility script install>>")</span></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"> #check for python version </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6):</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Python version is %s. harvest-tools requires at least 2.6"%(sys.version)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Python version is %s. harvest-tools requires at least 2.6"%(sys.version)))</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> sys.exit(1)</span>
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20
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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"> #complete shebang</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;">--- a/harvest-snps.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;">+++ b/harvest-snps.py</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> #print help/usage</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: harvest-snps.py <parsnp.hvt> [outfile]"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: harvest-snps.py <parsnp.hvt> [outfile]")</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> #check in path for harvest</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/harvest-variants.py</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/harvest-variants.py</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> #usage/help</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: harvest-variants.py <parsnp.hvt> [outfile]"</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: harvest-variants.py <parsnp.hvt> [outfile]")</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> #check in path for harvest</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;">--- a/src/harvest-alignments.py</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;">+++ b/src/harvest-alignments.py</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!python</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!python3</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> import os,sys,string,subprocess</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> ##harvest utility file for XMFA file(s) of core genome alignments</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span></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"> #print help/usage</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: harvest-alignments.py <parsnp.hvt> [outfile]"</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: harvest-alignments.py <parsnp.hvt> [outfile]")</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> #check in path for harvest</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;">--- a/src/harvest-backbone.py</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;">+++ b/src/harvest-backbone.py</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!python</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!python3</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> import os,sys,string,subprocess</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> ##harvest utility file for tab-delimited backbone file</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> #print help/usage</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: harvest-backbone.py <parsnp.hvt> [outfile]"</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: harvest-backbone.py <parsnp.hvt> [outfile]")</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> #check in path for harvest</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/harvest-phylogeny.py</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/harvest-phylogeny.py</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!python</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!python3</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> import os,sys,string,subprocess</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> ##harvest utility file for newick file of core genome phylogeny</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> #print help/usage</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: harvest-phylogeny.py <parsnp.hvt> [outfile]"</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: harvest-phylogeny.py <parsnp.hvt> [outfile]")</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> sys.exit(1)</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> #check in path for harvest</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/harvest-snps.py</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/harvest-snps.py</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!python</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!python3</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> import os,sys,string,subprocess</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> ##harvest utility file for multi-fasta file of SNP loci</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> #print help/usage</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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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 "usage: harvest-snps.py <parsnp.hvt> [outfile]"</span></span>
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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("usage: harvest-snps.py <parsnp.hvt> [outfile]")</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> sys.exit(1)</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> #check in path for harvest</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/harvest-variants.py</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/harvest-variants.py</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!python</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!python3</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> import os,sys,string,subprocess</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> ##harvest utility file for writing VCF file</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> #ROADMAP</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> #usage/help</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> if len(sys.argv) == 1 or sys.argv[1] in helpme:</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: harvest-variants.py <parsnp.hvt> [outfile]"</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: harvest-variants.py <parsnp.hvt> [outfile]")</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> #check in path for harvest</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,3 +4,4 @@ hardening.patch</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">remove_memwrap.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">parallel.patch</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">use-c++-14.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">python-2to3.patch</span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">@@ -22,3 +22,7 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Entry: harvesttools</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Repository: https://github.com/marbl/harvest-tools.git</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">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Repository-Browse: https://github.com/marbl/harvest-tools</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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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Bug-Database: https://github.com/marbl/harvest-tools/issues</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Bug-Submit: https://github.com/marbl/harvest-tools/issues/new</span></pre>
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