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GitLab

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<h3>

Étienne Mollier pushed to branch master

at <a href="https://salsa.debian.org/med-team/bioperl-run">Debian Med / bioperl-run</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/0c1e07eb30814d4a570cdb68879f46279f439780">0c1e07eb</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2022-02-10T20:03:27+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initialize changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/d09a2a1f75c9e8ebf3f0f1e72784ab19b7f67355">d09a2a1f</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2022-02-10T20:40:09+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch

Integration of newer muscle version in debian changed the code path in

the way the test may be skipped, breaking autopkgtest of bioperl-run.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/ff03d92ae69cbc48dae1bc7894399fe220d286f4">ff03d92a</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2022-02-10T20:44:07+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/c15b6b71b2d5113f8893463bf4c897f03ad2c744">c15b6b71</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2022-02-10T20:44:23+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move libmodule-build-perl from Build-Depends-Indep to Build-Depends.

Changes-By: lintian-brush

Fixes: lintian: libmodule-build-perl-needs-to-be-in-build-depends

See-also: https://lintian.debian.org/tags/libmodule-build-perl-needs-to-be-in-build-depends.html

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/ee00d3360a3607a279338e9b0c92f352eb47cec9">ee00d336</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2022-02-10T20:55:25+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>5 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>

</li>

<li class="file-stats">

<a href="#cb33929afa52e3ee6c6e7ec533daac5f7382c4a4">

<span class="new-file">

+

debian/patches/adjust-muscle-test.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#dc1f5566c6177a9c104f79b69030a79950d300d9">

<span class="deleted-file">

−

debian/patches/skip_tests_for_muscle.patch

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bioperl-run (1.7.3-8) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">    Integration of newer muscle version in debian changed the code path in</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    the way the test may be skipped, breaking autopkgtest of bioperl-run.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Move libmodule-build-perl from Build-Depends-Indep to Build-Depends.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org>  Thu, 10 Feb 2022 20:44:28 +0100</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">bioperl-run (1.7.3-7) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  * d/watch: fix broken link to github and adjust version mangling to fit</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,9 +6,8 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>

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6

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<td class="new_line diff-line-num" data-linenumber="6" 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="LC6" class="line" lang="plaintext">Section: science</span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>

</pre>

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9

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<td class="new_line diff-line-num old" 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">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13)</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13)<span class="idiff left right">, libmodule-build-perl</span></span>

</pre>

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Build-Depends-Indep: perl,</span>

</pre>

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11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">                     libmodule-build-perl,</span>

</pre>

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12

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">                     bioperl (>= 1.7.4),</span>

</pre>

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13

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># Recommended in Build.PL:</span>

</pre>

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14

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">                     libalgorithm-diff-perl,</span>

</pre>

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<br>

</li>

<li id="cb33929afa52e3ee6c6e7ec533daac5f7382c4a4">

<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9#cb33929afa52e3ee6c6e7ec533daac5f7382c4a4"><strong>debian/patches/adjust-muscle-test.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: adjust skip count for Muscle test</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The initial count looks like upstream might have forgotten to update it.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2022-02-10</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">---</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/t/Muscle.t</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/t/Muscle.t</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">     unless ( $version >= 3.6 ) {</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">         skip(</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> "Only muscle version 3.6 or higher is supported by these tests. Skipping tests",</span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            7</span></span>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            10</span></span>

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16

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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="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">         exit(0);</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">     }</span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -88,4 +88,4 @@</span></span>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff">     is( $s1_perid == 41 || $s1_perid == 42,</span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff">         1, 'diff versions of MUSCLE have different vals' );</span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>

</pre>

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25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span></pre>

</td>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,6 @@ skip_tests_for_wise.patch</td>

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<td class="old_line diff-line-num" 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">

7

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<td class="new_line diff-line-num" 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">skip_tests_for_phylip.patch</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="8" 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">

8

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<td class="new_line diff-line-num" data-linenumber="8" 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">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">skip_tests_for_phyml.patch</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" 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">

9

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<td class="new_line diff-line-num" data-linenumber="9" 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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">skip_tests_for_infernal.patch</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="10" 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">

10

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<td class="new_line diff-line-num old" data-linenumber="10" 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="LC10" class="line" lang="plaintext">skip_tests_for_muscle.patch</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" 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">

11

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<td class="new_line diff-line-num" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">skip_tests_for_ncbi-blast+.patch</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" 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">

12

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<td class="new_line diff-line-num" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">hyphy.patch</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="13" 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">

13

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<td class="new_line diff-line-num" data-linenumber="12" 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">

12

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">remove_tests_for_ensembl.patch</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,3 +17,4 @@ skip-test-for-kalign.patch</td>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="new_line diff-line-num" 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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">fix-whatis-entries.patch</span>

</pre>

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19

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18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">unscramble-erpin.patch</span>

</pre>

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20

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">fix-pod-conversion.patch</span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">adjust-muscle-test.patch</span></pre>

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<br>

</li>

<li id="dc1f5566c6177a9c104f79b69030a79950d300d9">

<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9#dc1f5566c6177a9c104f79b69030a79950d300d9"><strong>debian/patches/skip_tests_for_muscle.patch</strong>

deleted

</a>

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1

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>

</pre>

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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, 16 Dec 2016 09:17:37 +0100</span></span>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Exclude some failed test when using muscle.  Seems Debian's muscle is newer</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/t/Muscle.t</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/t/Muscle.t</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span> use strict;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> BEGIN {</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">     use Bio::Root::Test;</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;">-    test_begin( -tests => 16 );</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;">+    test_begin( -tests => 8 );</span></span>

</pre>

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13

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">     use_ok('Bio::Tools::Run::Alignment::Muscle');</span>

</pre>

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14

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">     use_ok('Bio::AlignIO');</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">     use_ok('Bio::SeqIO');</span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -39,10 +39,6 @@</span> SKIP: {</span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">     }</span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">     cmp_ok( $version, '>=', 3.6, "Code tested only on muscle versions > 3.6" );</span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    $aln = $factory->align($inputfilename);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    ok($aln);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is( $aln->num_sequences, 7 );</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff">     my $str = Bio::SeqIO->new(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff">         -file   => test_input_file("cysprot.fa"),</span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">         -format => 'Fasta'</span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -53,11 +49,11 @@</span> SKIP: {</span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">     }</span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff">     my $seq_array_ref = \@seq_array;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    $aln = $factory->align($seq_array_ref);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is $aln->num_sequences, 7;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    my $s1_perid = POSIX::ceil( $aln->average_percentage_identity );</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is( $s1_perid == 43 || $s1_perid == 44,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        1, 'diff versions of MUSCLE have different vals' );</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #$aln = $factory->align($seq_array_ref);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #is $aln->num_sequences, 7;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #my $s1_perid = POSIX::ceil( $aln->average_percentage_identity );</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #is( $s1_perid == 43 || $s1_perid == 44,</span></span>

</pre>

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40

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #    1, 'diff versions of MUSCLE have different vals' );</span></span>

</pre>

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41

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> </span>

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42

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff">     my $logfile = test_output_file();</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="43" 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">

43

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">     my $outfile = test_output_file();</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="44" 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">

44

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -75,17 +71,18 @@</span> SKIP: {</span>

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45

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff">     );</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="46" 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">

46

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff">     $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);</span>

</pre>

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47

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff">     is( $factory->log, $logfile, 'log file' );</span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    $aln = $factory->align($seq_array_ref);</span></span>

</pre>

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49

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is $aln->num_sequences, 7;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="50" 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">

50

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    $s1_perid = POSIX::ceil( $aln->average_percentage_identity );</span></span>

</pre>

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51

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is( $s1_perid == 43 || $s1_perid == 44,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="52" 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="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        1, 'diff versions of MUSCLE have different vals' );</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #$aln = $factory->align($seq_array_ref);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #is $aln->num_sequences, 7;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #$s1_perid = POSIX::ceil( $aln->average_percentage_identity );</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #is( $s1_perid == 43 || $s1_perid == 44,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="57" 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="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #    1, 'diff versions of MUSCLE have different vals' );</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="58" 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="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    my $s1_perid;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="59" 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="LC59" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="60" 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="LC60" class="line" lang="diff">     $inputfilename = test_input_file("cysprot1a.fa");</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="61" 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="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    $aln           = $factory->align($inputfilename);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="62" 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">

62

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is $aln->num_sequences, 3;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="63" 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">

63

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    $s1_perid = POSIX::ceil( $aln->average_percentage_identity );</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="64" 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">

64

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="65" 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">

65

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    is( $s1_perid == 41 || $s1_perid == 42,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="66" 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">

66

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        1, 'diff versions of MUSCLE have different vals' );</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="67" 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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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="68" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="69" 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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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #$aln           = $factory->align($inputfilename);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="70" 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">

70

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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #is $aln->num_sequences, 3;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="71" 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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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #$s1_perid = POSIX::ceil( $aln->average_percentage_identity );</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="72" 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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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="73" 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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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #is( $s1_perid == 41 || $s1_perid == 42,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="74" 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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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #    1, 'diff versions of MUSCLE have different vals' );</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="75" 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="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span></pre>

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