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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tree-puzzle">Debian Med / tree-puzzle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/commit/79f003fb0036253d5079345367fce152066db057">79f003fb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-16T08:51:06Z</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/tree-puzzle/commit/77f8022fd5ae2c6924357e7c778489b61d73335f">77f8022f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-16T08:51:45Z</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/tree-puzzle/commit/16e330a33861fac1679fb15d79b44d107d2fc4f2">16e330a3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-16T08:51:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/commit/14434262102907134ecf53cca6e0b59d0461833d">14434262</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-16T08:54:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix doc location (as per debhelper 11)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/commit/c2724d78ffa14f057a8f0e3d01c33896509dd70e">c2724d78</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-16T09:04:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some spelling issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/commit/199cedb4c92e5bf05f78f5aa76b5b8d4642706e2">199cedb4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-16T09:08:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 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="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
<span class="new-file">
+
debian/patches/spelling.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#27f33d7c5a1a705506e665408e9d72937578a4a9">
debian/tree-puzzle-doc.doc-base
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tree-puzzle (5.2-11) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debhelper 11</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new 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: 4.2.1</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Fix some spelling issues</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 16 Oct 2018 11:06:43 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">tree-puzzle (5.2-10) unstable; urgency=medium</span>
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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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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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="plaintext"> * Do not try parallel builds</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<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">@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Charles Plessy <plessy@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libopenmpi-dev,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libsprng2-dev</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1</span>.1</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/tree-puzzle.git</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/tree-puzzle.git</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/tree-puzzle</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/tree-puzzle.git</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: http://www.tree-puzzle.de</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: tree-puzzle</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">20_no_copy_of_sprng.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">tests-need-bash.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spelling.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix some spelling issues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Tue, 16 Oct 2018 10:51:06 +0200</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/ml2.c</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/ml2.c</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -417,7 +417,7 @@ Node *internalnode(Tree *tr, char **chpp</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> if (!strcmp(ident, idcomp)) {</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> if (usedtaxa[i]) {</span>
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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;">- fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence '");</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurrence of sequence '");</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> fprintf(STDOUT, "%s' in tree)\n\n\n", ident);</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # if PARALLEL</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> PP_Finalize();</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/puzzle1.c</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/puzzle1.c</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1967,7 +1967,7 @@ void initps(FILE *ofp)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> /* PS definition of a centered print */</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> fprintf(ofp, "/centershow {\n");</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> fprintf(ofp, " dup stringwidth pop %% get length of string\n");</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(ofp, " -2 div %% devide length by -2\n");</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(ofp, " -2 div %% divide length by -2\n");</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> fprintf(ofp, " 0 rmoveto %% move half width to left\n");</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> fprintf(ofp, " show\n");</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> fprintf(ofp, "} def\n");</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3538,7 +3538,7 @@ void writeoutputfile(FILE *ofp, int part</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> i+1, Rates[i], (1.0-fracinv)/(double) numcats); </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(ofp, "\nCategories 1-%d approximate a continous ", numcats);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(ofp, "\nCategories 1-%d approximate a continuous ", numcats);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> fprintf(ofp, "Gamma-distribution with expectation 1\n"); </span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> fprintf(ofp, "and variance ");</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> if (Geta == 1.0) fprintf(ofp, "infinity");</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5231,21 +5231,21 @@ void printusagehhh(char *fname)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> #ifdef HHH</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> /* |<--- 80 characters --->| */</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> fprintf(stderr, " not yet implemented in this version:\n");</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wslb - write site lhs to PREFIX.sitelhb (binary) [not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wsrb - write site rates to PREFIX.siterateb (binary) [not yet]\n");</span></span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wparam - write params to PREFIX.param [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -qsupport - prints quartet support for incorporated splits [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -consth=<#> - consensus threshold, e.g. 50=M_50 consensus [not yet]\n");</span></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wqnex - write quartets in nexus format [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wsnex - write splits in nexus format [not yet]\n");</span></span>
</pre>
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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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wsth=<#> - split threshold, e.g. 50 - splits of the M_50 [not yet]\n");</span></span>
</pre>
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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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -wsnex=<#> - write splits with > <#>%% occurence - nexus format[not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -witnex - write intermediate trees in nexus format [not yet]\n");</span></span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -quartml - use ML values to evaluate quartets [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -quartmlapprox - use approximate ML values to evaluate quartets [default]\n");</span></span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -quartnj - use NJ to evaluate quartets [not yet]\n");</span></span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -quartme - use ME to evaluate quartets [not yet]\n");</span></span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " -quartpars - use parsimony to evaluate quartets [not yet]\n");</span></span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wslb - write site lhs to PREFIX.sitelhb (binary) [not yet]\n");</span></span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wsrb - write site rates to PREFIX.siterateb (binary) [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wparam - write params to PREFIX.param [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -qsupport - prints quartet support for incorporated splits [not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -consth=<#> - consensus threshold, e.g. 50=M_50 consensus [not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wqnex - write quartets in nexus format [not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wsnex - write splits in nexus format [not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wsth=<#> - split threshold, e.g. 50 - splits of the M_50 [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -wsnex=<#> - write splits with > <#>%% occurrence - nexus format[not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -witnex - write intermediate trees in nexus format [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -quartml - use ML values to evaluate quartets [not yet]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -quartmlapprox - use approximate ML values to evaluate quartets [default]\n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -quartnj - use NJ to evaluate quartets [not yet]\n");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -quartme - use ME to evaluate quartets [not yet]\n");</span></span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " -quartpars - use parsimony to evaluate quartets [not yet]\n");</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> fprintf(stderr, "\n");</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> #endif /* HHH */</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/puzzle2.c</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/puzzle2.c</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -68,7 +68,7 @@ void readid(FILE *infp, int t)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> if (Identif[t][j] != Identif[i][j])</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> flag = FALSE;</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> if (flag) {</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence name '");</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurrence of sequence name '");</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> fputid(STDOUT, t);</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> fprintf(STDOUT, "')\n\n\n");</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> # if PARALLEL</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/treesort.c</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/treesort.c</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -601,7 +601,7 @@ treelistitemtype *addtree2list(char</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> /**********/</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/* resort list of trees by number of occurences for output */</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* resort list of trees by number of occurrences for output */</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> void sortbynum(treelistitemtype *list, treelistitemtype **sortlist)</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> {</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> treelistitemtype *tmpptr = NULL;</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -721,9 +721,9 @@ void fprintfsortedpstrees(FILE *output,</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> if (num == 1){</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> fprintf (output, "\n");</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> fprintf (output, "The following tree(s) occured in more than %.2f%% of the %d puzzling steps.\n", cutoff, itemsum);</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf (output, "The trees are orderd descending by the number of occurences.\n");</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf (output, "The trees are orderd descending by the number of occurrences.\n");</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> fprintf (output, "\n");</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf (output, "\n occurences ID Phylip tree\n");</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf (output, "\n occurrences ID Phylip tree\n");</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> fprintf (output, "%2d. %5d %6.2f%% %5d ", num++, (*tmpptr).count, percent, (*tmpptr).id);</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2#27f33d7c5a1a705506e665408e9d72937578a4a9"><strong>debian/tree-puzzle-doc.doc-base</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,4 +6,4 @@ Abstract: Maximum likelihood analysis for nucleotide, amino acid, and two-state</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: Science/Biology</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Format: pdf</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Files: /usr/share/doc/tree-puzzle<span class="idiff left right">-doc</span>/tree-puzzle.pdf</span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Files: /usr/share/doc/tree-puzzle/tree-puzzle.pdf</span></pre>
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