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GitLab

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<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/murasaki/commit/e5bac3e143b97c22d064d1a6aeeb9235956b38ab">e5bac3e1</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-14T09:23:08+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/murasaki/commit/649aedbc9cf2d63d8cd6c971548ffd4b493d361c">649aedbc</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-14T09:23:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/murasaki/commit/197362d606fbacfe72d85f15f819554ff568264c">197362d6</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-14T09:23:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.5

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/murasaki/commit/5dfa90a025cbeb425bcaf7de0a71a3070ddc6ebd">5dfa90a0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-14T15:48:15+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix remaining spelling issues

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/murasaki/commit/3f04adbfc8936177fa53e1a38fdbe1f559ec6c66">3f04adbf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-14T15:54:21+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/murasaki/commit/d963713feafb191ef4e34b254ef15b59bf10b0e6">d963713f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-14T15:58:53+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">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="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

debian/compat

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

debian/patches/spelling.patch

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">murasaki (1.68.6-7) unstable; urgency=medium</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

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

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

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * debhelper 11</span>

</pre>

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

</td>

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

4

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>

</pre>

</td>

</tr>

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

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

</td>

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

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.1.5</span>

</pre>

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</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Fix remaining spelling issues</span>

</pre>

</td>

</tr>

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

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

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * d/rules: Do not parse d/changelog</span>

</pre>

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

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

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

</tr>

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

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

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Sat, 14 Jul 2018 15:54:27 +0200</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">murasaki (1.68.6-6) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" 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

</td>

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

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

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  [ Gert Wollny ]</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

<hr>

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

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<td class="diff-line-num old old_line" data-linenumber="1" 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">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">9</span></span></pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

1

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">11</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>

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<td class="diff-line-num old_line" data-linenumber="3" 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="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>

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<td class="diff-line-num old_line" data-linenumber="5" 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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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span> <span class="p">(>=</span> <span class="m" style="color: #099;"><span class="idiff left right">9</span></span><span class="p">),</span></span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span> <span class="p">(>=</span> <span class="m" style="color: #099;"><span class="idiff left">11</span></span><span class="p"><span class="idiff right">~</span>),</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel">               <span class="n" style="color: #333;">libboost</span><span class="p">-</span><span class="n" style="color: #333;">regex</span><span class="p">-</span><span class="n" style="color: #333;">dev</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel">               <span class="n" style="color: #333;">libboost</span><span class="p">-</span><span class="n" style="color: #333;">iostreams</span><span class="p">-</span><span class="n" style="color: #333;">dev</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel">               <span class="n" style="color: #333;">libboost</span><span class="p">-</span><span class="n" style="color: #333;">filesystem</span><span class="p">-</span><span class="n" style="color: #333;">dev</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,9 +12,9 @@ Build-Depends: debhelper (>= 9),</td>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel">               <span class="n" style="color: #333;">libcrypto</span><span class="p">++-</span><span class="n" style="color: #333;">dev</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel">               <span class="n" style="color: #333;">libpstreams</span><span class="p">-</span><span class="n" style="color: #333;">dev</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel">               <span class="n" style="color: #333;">libopenmpi</span><span class="p">-</span><span class="n" style="color: #333;">dev</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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="diff-line-num new_line old" data-linenumber="15" 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="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;"><span class="idiff left right">3.9.8</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;"><span class="idiff left">anonscm</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">cgit</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">murasaki</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">git</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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="diff-line-num new_line old" data-linenumber="15" 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="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;"><span class="idiff left">anonscm</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">git</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">med</span></span><span class="p">/</span><span class="n" style="color: #333;">murasaki</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;"><span class="idiff left right">4.1.5</span></span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;"><span class="idiff left">salsa</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">team</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff right">murasaki</span></span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;"><span class="idiff left">salsa</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">team</span></span><span class="p">/</span><span class="n" style="color: #333;">murasaki</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>

</pre>

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

18

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">murasaki</span><span class="p">.</span><span class="n" style="color: #333;">dna</span><span class="p">.</span><span class="n" style="color: #333;">bio</span><span class="p">.</span><span class="n" style="color: #333;">keio</span><span class="p">.</span><span class="n" style="color: #333;">ac</span><span class="p">.</span><span class="n" style="color: #333;">jp</span><span class="p">/</span><span class="n" style="color: #333;">wiki</span><span class="p">/</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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19

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">murasaki</span></span>

</pre>

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</table>

<br>

</li>

<li id="45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<a href="https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>

<hr>

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

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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">@@ -4,6 +4,24 @@ Description: Spelling fixes</td>

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<td class="diff-line-num 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">

4

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<td class="diff-line-num 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">

4

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/murasaki.1</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num 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">

6

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/murasaki.1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -338,7 +338,7 @@ Use gapped (true) or ungapped (false (de</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> .IP "\-\-scorebyminimumpair <B>" 4</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

9

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> .IX Item "--scorebyminimumpair <B>"</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Do anchor scoring by minimum pair when appropriate</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-(default). Alternative is arithmatic mean (seldom useful, but</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+(default). Alternative is arithmetic mean (seldom useful, but</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> theoretically faster).</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> =item \-\-rifts|\-/ <D></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> .Sp</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -360,7 +360,7 @@ Use gapped (true) or ungapped (false (de</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> .IP "\-\-scorebyminimumpair <B>" 4</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> .IX Item "--scorebyminimumpair <B>"</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> Do anchor scoring by minimum pair when appropriate</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-(default). Alternative is arithmatic mean (seldom useful, but</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+(default). Alternative is arithmetic mean (seldom useful, but</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> theoretically faster).</span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> .SS "Output options"</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> .IX Subsection "Output options"</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -521,7 +521,7 @@ over the network (helpful for slow netwo</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> .IX Item "--mpidistro|-L <B>"</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> Toggles use of \s-1MPI\s0 to distribute sequence data over (if the sequence</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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="42" 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">@@ -24,8 +42,53 @@ Description: Spelling fixes</td>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> .IP "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently." 4</span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> .IX Item "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently."</span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> .RE</span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -628,7 +628,7 @@ this problem.</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> .SS ".anchors files"</span>

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="diff"> .IX Subsection ".anchors files"</span>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="diff"> These files are 1 anchor per line, with a 3\-tuple per sequence. Each</span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-touple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tuple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> anchored interval on each sequence. The sequence order matches that of</span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> the order in the .seqs file. The coordinates are structured such that</span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> 1 refers to the first base in the sequence, 2 to the second,</span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -653,7 +653,7 @@ second sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> This is an antiquated file format, but used by \s-1GMV\s0 to calculate</span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> statistics like TF-IDF scores, and has been kept around for that</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> reason. The .anchors.details file has the same format and information</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-as the .anchors file, however after the anchor touples are two more</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+as the .anchors file, however after the anchor tuples are two more</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> terms: a score, and a comma (,) delimited list of term and count pairs</span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> (written \*(L"term:count\*(R"). The score and count data might be varied</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> depending on the \f(CW\*(C`\-\-histogram\*(C'\fR option choices.</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -699,7 +699,7 @@ by a blank line. A repeat record looks l</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> The first line (always prefixed \*(L"R:\*(R") shows the repeating seed itself</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> (where the . are the bases masked by the pattern). The subsequent</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lines show where these seeds occured in the input sequences (in the</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lines show where these seeds occurred in the input sequences (in the</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> first (0) and second (1) sequences). Note that if there are no hits in</span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> a particular sequence, it doesn't include a blank line for that sequence. For example:</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> .PP</span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/murasaki.html</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/murasaki.html</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -326,7 +326,7 @@ parameter).</p></span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> <dd></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> <p>Do anchor scoring by minimum pair when appropriate</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;">-(default). Alternative is arithmatic mean (seldom useful, but</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;">+(default). Alternative is arithmetic mean (seldom useful, but</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> theoretically faster).</span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> =item --rifts|-/ &lt;D&gt;</p></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> <p>Allow anchors to skip D sequences (default 0).</p></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -357,7 +357,7 @@ parameter).</p></span></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"> <dd></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> <p>Do anchor scoring by minimum pair when appropriate</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-(default). Alternative is arithmatic mean (seldom useful, but</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+(default). Alternative is arithmetic mean (seldom useful, but</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> theoretically faster).</p></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </dd></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </dl></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -606,7 +606,7 @@ is too high.</p></span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="diff"> <dt><strong><a name="memorybalance_a_b" class="item">--memorybalance|-a &lt;B&gt;</a></strong></dt></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="diff"> </span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,8 +98,53 @@ Description: Spelling fixes</td>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"> the amount of available ram.</strong></dt></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> <dt><strong><a name="if_no_distribute_storage_evently_this_more_likely_to_achieve_optimal_run_times_but_might_not_utilize_memory_as_efficiently" class="item">If no: distribute storage evently. This more likely to achieve</span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -697,7 +697,7 @@ this problem.</p></span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </p></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> <h2><a name="_anchors_files">.anchors files</a></h2></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> <p>These files are 1 anchor per line, with a 3-tuple per sequence. Each</span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-touple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tuple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> anchored interval on each sequence. The sequence order matches that of</span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> the order in the .seqs file. The coordinates are structured such that</span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> 1 refers to the first base in the sequence, 2 to the second,</span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -719,7 +719,7 @@ second sequence.</p></span></span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> <p>This is an antiquated file format, but used by <em>GMV</em> to calculate</span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> statistics like TF-IDF scores, and has been kept around for that</span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> reason. The .anchors.details file has the same format and information</span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-as the .anchors file, however after the anchor touples are two more</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+as the .anchors file, however after the anchor tuples are two more</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> terms: a score, and a comma (,) delimited list of term and count pairs</span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> (written &quot;term:count&quot;). The score and count data might be varied</span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> depending on the <a href="#histogram"><code>--histogram</code></a> option choices.</p></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -764,7 +764,7 @@ by a blank line. A repeat record looks l</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff">  1: 2480929222 -1874514626 2543723555 -2550045172</pre></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> <p>The first line (always prefixed &quot;R:&quot;) shows the repeating seed itself</span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> (where the . are the bases masked by the pattern). The subsequent</span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lines show where these seeds occured in the input sequences (in the</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lines show where these seeds occurred in the input sequences (in the</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> first (0) and second (1) sequences). Note that if there are no hits in</span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> a particular sequence, it doesn't include a blank line for that sequence. For example:</p></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> <pre></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/murasaki.pod</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/murasaki.pod</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -233,7 +233,7 @@ Use gapped (true) or ungapped (false (de</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> =item --scorebyminimumpair <B></span>

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> Do anchor scoring by minimum pair when appropriate</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-(default). Alternative is arithmatic mean (seldom useful, but</span></span>

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+(default). Alternative is arithmetic mean (seldom useful, but</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> theoretically faster).</span>

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> =item --rifts|-/ <D></span>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -260,7 +260,7 @@ Use gapped (true) or ungapped (false (de</span></span>

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> =item --scorebyminimumpair <B></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> Do anchor scoring by minimum pair when appropriate</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-(default). Alternative is arithmatic mean (seldom useful, but</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+(default). Alternative is arithmetic mean (seldom useful, but</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> theoretically faster).</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> =back</span>

</pre>

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40

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<td class="diff-line-num new_line" data-linenumber="148" 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="LC148" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -486,7 +486,7 @@ Assign hashers to large memory nodes fir</span></span>

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41

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="diff"> </span>

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<td class="diff-line-num old_line" data-linenumber="42" 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">

42

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="diff"> =over</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,8 +154,53 @@ Description: Spelling fixes</td>

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46

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="diff"> the amount of available ram.</span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"> =item If no: distribute storage evently. This more likely to achieve</span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -577,7 +577,7 @@ this problem.</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> =head2 .anchors files</span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> These files are 1 anchor per line, with a 3-tuple per sequence. Each</span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-touple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tuple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> anchored interval on each sequence. The sequence order matches that of</span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> the order in the .seqs file. The coordinates are structured such that</span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> 1 refers to the first base in the sequence, 2 to the second,</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -601,7 +601,7 @@ second sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> This is an antiquated file format, but used by L<GMV> to calculate</span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> statistics like TF-IDF scores, and has been kept around for that</span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> reason. The .anchors.details file has the same format and information</span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-as the .anchors file, however after the anchor touples are two more</span></span>

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+as the .anchors file, however after the anchor tuples are two more</span></span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> terms: a score, and a comma (,) delimited list of term and count pairs</span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> (written "term:count"). The score and count data might be varied</span>

</pre>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> depending on the C<--histogram> option choices.</span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -648,7 +648,7 @@ by a blank line. A repeat record looks l</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> The first line (always prefixed "R:") shows the repeating seed itself</span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> (where the . are the bases masked by the pattern). The subsequent</span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lines show where these seeds occured in the input sequences (in the</span></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lines show where these seeds occurred in the input sequences (in the</span></span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> first (0) and second (1) sequences). Note that if there are no hits in</span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> a particular sequence, it doesn't include a blank line for that sequence. For example:</span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>

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49

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/murasaki.txt</span></span>

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50

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/murasaki.txt</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -200,7 +200,7 @@ OPTIONS</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff">     --scorebyminimumpair <B></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff">         Do anchor scoring by minimum pair when appropriate (default).</span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        Alternative is arithmatic mean (seldom useful, but theoretically</span></span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        Alternative is arithmetic mean (seldom useful, but theoretically</span></span>

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff">         faster). =item --rifts|-/ <D></span>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff">         Allow anchors to skip D sequences (default 0).</span>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -221,7 +221,7 @@ OPTIONS</span></span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff">     --scorebyminimumpair <B></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff">         Do anchor scoring by minimum pair when appropriate (default).</span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        Alternative is arithmatic mean (seldom useful, but theoretically</span></span>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        Alternative is arithmetic mean (seldom useful, but theoretically</span></span>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff">         faster).</span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff">   Output options</span>

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51

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -372,7 +372,7 @@ OPTIONS</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="diff">     --memorybalance|-a <B></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="210" 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">@@ -57,6 +210,33 @@ Description: Spelling fixes</td>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="diff">         amount of available ram.</span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="diff">         If no: distribute storage evently. This more likely to achieve</span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="diff">         optimal run times, but might not utilize memory as efficiently.</span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -428,7 +428,7 @@ FILE FORMATS</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff">   .anchors files</span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff">     These files are 1 anchor per line, with a 3-tuple per sequence. Each</span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    touple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    tuple represents the start and stop coordinates and strand of the</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff">     anchored interval on each sequence. The sequence order matches that of</span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff">     the order in the .seqs file. The coordinates are structured such that 1</span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff">     refers to the first base in the sequence, 2 to the second, etc. Negative</span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -450,7 +450,7 @@ FILE FORMATS</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff">     This is an antiquated file format, but used by GMV to calculate</span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff">     statistics like TF-IDF scores, and has been kept around for that reason.</span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff">     The .anchors.details file has the same format and information as the</span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    .anchors file, however after the anchor touples are two more terms: a</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    .anchors file, however after the anchor tuples are two more terms: a</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff">     score, and a comma (,) delimited list of term and count pairs (written</span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff">     "term:count"). The score and count data might be varied depending on the</span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff">     "--histogram" option choices.</span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -493,7 +493,7 @@ FILE FORMATS</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff">     The first line (always prefixed "R:") shows the repeating seed itself</span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff">     (where the . are the bases masked by the pattern). The subsequent lines</span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    show where these seeds occured in the input sequences (in the first (0)</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    show where these seeds occurred in the input sequences (in the first (0)</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff">     and second (1) sequences). Note that if there are no hits in a</span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff">     particular sequence, it doesn't include a blank line for that sequence.</span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff">     For example:</span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/murasaki.cc</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/murasaki.cc</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -303,7 +303,7 @@ void MurasakiRuntime::prep(){</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,3 +270,14 @@ Description: Spelling fixes</td>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="diff">     but they  do affect the visible range, and thus causes some scrunching.</span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="diff">  "--showall=scale" manually sets to the X and Y ranges to the range of the</span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="diff">     data (so 1's are visibly different from 0's).</span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/simpal.pl</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/simpal.pl</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -272,7 +272,7 @@ simpal.pl [options] <ref seq> <target se</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> maxLoop -- specifies max separation for the ends of the palindromes</span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> maxDistance -- specifies the maximum difference in palindrome length</span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff">                when comparing palindromes</span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-tolerance -- max permissable misses in palindromes between sequences</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tolerance -- max permissible misses in palindromes between sequences</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> Setting either to -1 means no limit</span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/murasaki/compare/f70f15204db1582601977c87b7e24630248b8367...d963713feafb191ef4e34b254ef15b59bf10b0e6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># Copyright 2015 Andreas Tille</span>

</pre>

</td>

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<td class="diff-line-num 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">

4

</td>

<td class="diff-line-num 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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># GPL</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">DEBPKGNAME    := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">DEBMEDBIN     := debian/$(DEBPKGNAME)-common/usr/lib/debian-med/bin</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">MANDIR                := debian/$(DEBPKGNAME)/usr/share/man/man1</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">CMANDIR               := debian/$(DEBPKGNAME)-common/usr/share/man/man1</span>

</pre>

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<td class="diff-line-num old old_line" 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

</td>

<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">MMANDIR              := debian/$(DEBPKGNAME)-mpi/usr/share/man/man1</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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">

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">DEBMEDBIN     := debian/$(DEB_SOURCE)-common/usr/lib/debian-med/bin</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<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">

9

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">MANDIR                := debian/$(DEB_SOURCE)/usr/share/man/man1</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">CMANDIR              := debian/$(DEB_SOURCE)-common/usr/share/man/man1</span>

</pre>

</td>

</tr>

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

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

</td>

<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">

11

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">MMANDIR              := debian/$(DEB_SOURCE)-mpi/usr/share/man/man1</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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

<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>

</pre>

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<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># leads to linking failure:</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" 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="45" 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">@@ -44,8 +45,8 @@ override_dh_link:</td>

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

44

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<td class="diff-line-num new_line" data-linenumber="45" 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">

45

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

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">override_dh_install-arch:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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

<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">     dh_install -a</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="diff-line-num new_line" data-linenumber="47" 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">

47

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">     # using wildcards in install files is practical but it duplicates some files</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC47" class="line" lang="plaintext">     find debian/$(DEB<span class="idiff left right">PKGNAM</span>E)/usr -name "*-mpi" -delete</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">     find debian/$(DEB<span class="idiff left right">_SOURC</span>E)/usr -name "*-mpi" -delete</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" 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">

48

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<td class="diff-line-num new_line" data-linenumber="49" 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">

49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="49" 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">

49

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

50

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">override_dh_fixperms-indep:</span>

</pre>

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

50

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<td class="diff-line-num new_line" data-linenumber="51" 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">

51

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">     dh_fixperms -i</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" 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">

51

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<td class="diff-line-num new_line 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="LC51" class="line" lang="plaintext">     chmod a+x debian/$(DEB<span class="idiff left right">PKGNAM</span>E)-common/usr/share/perl5/murasaki/config.pl</span></pre>

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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">     chmod a+x debian/$(DEB<span class="idiff left right">_SOURC</span>E)-common/usr/share/perl5/murasaki/config.pl</span></pre>

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