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<h3>

Shayan Doust pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/pplacer/-/commit/d71eaaeb12f9ce57c7b8a1f935b46dd9f92eb4fa">d71eaaeb</a></strong>

<div>

<span>by Ralf Treinen</span>

<i>at 2020-06-13T21:08:51+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update patch for using ocaml bytes

</pre>

</li>

</ul>

<h4>1 changed file:</h4>

<ul>

<li class="file-stats">

<a href="#a4416d0924d117bd51912929ec975e7d1e789fd2">

debian/patches/ocaml_bytes

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a4416d0924d117bd51912929ec975e7d1e789fd2">

<a href="https://salsa.debian.org/med-team/pplacer/-/commit/d71eaaeb12f9ce57c7b8a1f935b46dd9f92eb4fa#a4416d0924d117bd51912929ec975e7d1e789fd2"><strong>debian/patches/ocaml_bytes</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,10 +2,10 @@ Author: Ralf Treinen <treinen@debian.org></td>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: ocaml strings are immutable in recent ocaml versions,</span></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">  replace them by Bytes.t where necessary</span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Index: pplacer/common_src/ppatteries.ml</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/common_src/ppatteries.ml</span>

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/common_src/ppatteries.ml   2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/common_src/ppatteries.ml        2020-06-13 18:46:39.670407109</span> +0200</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/common_src/ppatteries.ml       2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">-1.1~alpha19/common_src/ppatteries.ml    2020-06-13 18:52:51.000000000</span> +0200</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> let maybe_cons o l = maybe_map_cons identity o l</span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="37" 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">@@ -37,10 +37,10 @@ Index: pplacer/common_src/ppatteries.ml</td>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff">     new_s</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> end</span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/json_src/json.ml</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/json_src/json.ml</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/json_src/json.ml  2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/json_src/json.ml       2020-06-13 18:46:39.670407109</span> +0200</span></span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/json_src/json.ml      2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">-1.1~alpha19/json_src/json.ml   2020-06-13 18:52:51.000000000</span> +0200</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="p">@@ -72,7 +72,7 @@</span></span>

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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">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> let to_file name o =</span>

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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">

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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">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff">   let file = MaybeZipped.open_out name in</span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,10 +50,10 @@ Index: pplacer/json_src/json.ml</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff">     (fun () -> IO.flush file)</span>

</pre>

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<td class="diff-line-num old_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">

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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">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff">   in</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" 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="LC52" class="line" lang="diff">   to_formatter formatter o;</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="53" 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="LC53" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/common_src/alignment.ml</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" 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="LC53" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/common_src/alignment.ml</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="54" 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="LC54" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" 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="55" 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="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/common_src/alignment.ml   2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="55" 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="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/common_src/alignment.ml        2020-06-13 18:46:39.670407109</span> +0200</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/common_src/alignment.ml       2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">-1.1~alpha19/common_src/alignment.ml    2020-06-13 18:52:51.000000000</span> +0200</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="p">@@ -102,7 +102,7 @@</span></span>

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<td class="diff-line-num old_line" data-linenumber="58" 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="58" 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="LC58" class="line" lang="diff">   Printf.fprintf ch "%d %d\n" (n_seqs align) (length align);</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" 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="59" 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="LC59" class="line" lang="diff">   Array.iter (</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" 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="63" 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">@@ -63,10 +63,10 @@ Index: pplacer/common_src/alignment.ml</td>

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<td class="diff-line-num old_line" data-linenumber="63" 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="63" 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="LC63" class="line" lang="diff">   ) align;</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" 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="64" 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="LC64" class="line" lang="diff">   close_out ch</span>

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<td class="diff-line-num old_line" data-linenumber="65" 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="65" 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="LC65" class="line" lang="diff"> </span>

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<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/string_matrix.ml</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/pplacer_src/string_matrix.ml</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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="67" 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="LC67" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/pplacer_src/string_matrix.ml      2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/pplacer_src/string_matrix.ml   2020-06-13 18:46:39.670407109</span> +0200</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" 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="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/pplacer_src/string_matrix.ml  2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" 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="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">-1.1~alpha19/pplacer_src/string_matrix.ml       2020-06-13 18:52:51.000000000</span> +0200</span></span>

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<td class="diff-line-num old_line" data-linenumber="70" 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="70" 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="LC70" class="line" lang="diff"><span class="p">@@ -50,7 +50,7 @@</span></span>

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<td class="diff-line-num old_line" data-linenumber="71" 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="LC71" class="line" lang="diff"> let m = add_names [|"a";"b"|] [|[|"0";"1"|];[|"2";"3"|]|]</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" 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="72" 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="LC72" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" 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="76" 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">@@ -76,10 +76,10 @@ Index: pplacer/pplacer_src/string_matrix.ml</td>

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<td class="diff-line-num old_line" data-linenumber="76" 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="LC76" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" 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="77" 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="LC77" class="line" lang="diff"> let write_row ch row =</span>

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<td class="diff-line-num old_line" data-linenumber="78" 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="LC78" class="line" lang="diff">   Printf.fprintf ch "%s\n" (row_to_str "  " row)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/pplacer_run.ml</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/pplacer_src/pplacer_run.ml</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/pplacer_src/pplacer_run.ml        2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/pplacer_src/pplacer_run.ml     2020-06-13 18:46:39.670407109</span> +0200</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/pplacer_src/pplacer_run.ml    2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"><span class="p">@@ -118,7 +118,7 @@</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff">           (seq'.[!pos] <- seq.[e];</span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff">            incr pos))</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" 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="98" 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>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"> </span>

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/json_src/jsonparse.mly</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/json_src/jsonparse.mly</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/json_src/jsonparse.mly   2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/json_src/jsonparse.mly        2020-06-13 18:46:39.670407109</span> +0200</span></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/json_src/jsonparse.mly       2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">-1.1~alpha19/json_src/jsonparse.mly    2020-06-13 18:52:51.000000000</span> +0200</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff">         | "t" -> "\t"</span>

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<td class="diff-line-num old_line" data-linenumber="107" 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="LC107" class="line" lang="diff">         | _ -></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" 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="111" 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">@@ -111,10 +111,10 @@ Index: pplacer/json_src/jsonparse.mly</td>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff">     ) s</span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> </span>

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<td class="diff-line-num old_line" data-linenumber="113" 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="LC113" class="line" lang="diff">   let add_to_hash h (s, v) = Hashtbl.add h s v; h</span>

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<td class="diff-line-num old old_line" data-linenumber="114" 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="LC114" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer/pplacer_src/multiprocessing.ml</span></span>

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<td class="diff-line-num new old_line" data-linenumber="115" 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="LC114" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer<span class="idiff left right">-1.1~alpha19</span>/pplacer_src/multiprocessing.ml</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<td class="diff-line-num old old_line" data-linenumber="116" 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="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">.orig/pplacer_src/multiprocessing.ml   2020-06-13 18:46:39.67440713</span>0 +0200</span></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">/pplacer_src/multiprocessing.ml        2020-06-13 18:48:07.406882567</span> +0200</span></span>

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<td class="diff-line-num new old_line" data-linenumber="118" 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="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer<span class="idiff left right">-1.1~alpha19.orig/pplacer_src/multiprocessing.ml       2020-06-13 18:52:38.00000000</span>0 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer<span class="idiff left right">-1.1~alpha19/pplacer_src/multiprocessing.ml    2020-06-13 18:52:51.000000000</span> +0200</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"><span class="p">@@ -71,11 +71,11 @@</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff">   in aux pipe_map</span>

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<td class="diff-line-num old_line" data-linenumber="120" 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="LC120" class="line" lang="diff"> </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" 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="147" 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">@@ -147,3 +147,49 @@ Index: pplacer/pplacer_src/multiprocessing.ml</td>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="diff">       | Done body, Needs_data (header, _) -></span>

</pre>

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<td class="diff-line-num old_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">         let obj = Marshal.from_string (header ^ body) 0 in</span>

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

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer-1.1~alpha19/pplacer_src/guppy_squash.ml</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer-1.1~alpha19.orig/pplacer_src/guppy_squash.ml 2020-06-13 18:52:51.000000000 +0200</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer-1.1~alpha19/pplacer_src/guppy_squash.ml      2020-06-13 21:02:42.674037660 +0200</span></span>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="diff"><span class="p">@@ -174,7 +174,7 @@</span></span>

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="diff">       Newick_gtree.to_file cluster_t (path cluster_tree_name);</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="diff">       let outdir = path mass_trees_dirname in mkdir outdir;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="diff">       let pad_width = find_zero_pad_width (IntMap.cardinal blobim) in</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" 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="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      let prefix_of_int i = Filename.concat outdir (zero_pad_int pad_width i) in</span></span>

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<td class="diff-line-num new new_line" data-linenumber="159" 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="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      let prefix_of_int i = Filename.concat outdir (Bytes.to_string (zero_pad_int pad_width i)) in</span></span>

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<td class="diff-line-num new new_line" data-linenumber="160" 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="LC160" class="line" lang="diff">       (* make a tax tree here then run mimic on it *)</span>

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<td class="diff-line-num new new_line" data-linenumber="161" 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="LC161" class="line" lang="diff">       let wpt infix t i =</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" 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="LC162" class="line" lang="diff">         self#write_pre_tree (prefix_of_int i) infix t</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="163" 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="LC163" class="line" lang="diff"><span class="p">@@ -217,8 +217,8 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" 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="LC164" class="line" lang="diff">         let (_, cluster_t, _) = our_make_cluster refpkgo mode_str boot_prl in</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" 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="LC165" class="line" lang="diff">         Newick_gtree.to_file</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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="166" 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="LC166" class="line" lang="diff">           cluster_t</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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="167" 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="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          (path ("cluster."^(zero_pad_int pad_width i)^".tre"));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" 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="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        dprintf "Finished bootstrap %s/%d\n" (zero_pad_int pad_width i) (List.length boots);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" 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="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          (path ("cluster."^(Bytes.to_string (zero_pad_int pad_width i))^".tre"));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        dprintf "Finished bootstrap %s/%d\n" (Bytes.to_string (zero_pad_int pad_width i)) (List.length boots);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff">       in</span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff">       match children with</span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff">       | 1 -> List.iter run_boot boots</span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gh" style="color: #999;">Index: pplacer-1.1~alpha19/pam_src/pam_solver.ml</span></span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- pplacer-1.1~alpha19.orig/pam_src/pam_solver.ml       2020-06-13 18:52:38.000000000 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ pplacer-1.1~alpha19/pam_src/pam_solver.ml    2020-06-13 21:05:17.174881638 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff">   let old_leaf_idx old = Array.findi ((=) (IntMap.find old transm)) leaf_arr</span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff">   and rtrans i = IntMap.find i rtransm</span>

</pre>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff">   and total_mass = I.total_mass mass in</span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  let keep_string = String.make (Array.length leaf_arr) '\000' in</span></span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  let keep_string = Bytes.make (Array.length leaf_arr) '\000' in</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff">   Option.may</span>

</pre>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff">     (IntSet.iter (fun leaf -> keep_string.[old_leaf_idx leaf] <- '\001'))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff">     keep;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="p">@@ -39,7 +39,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff">   |> Matrix.of_arrays</span>

</pre>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff">   (* rows are masses; columns are leaves. thus, we need to transpose *)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff">   |> Matrix.rect_transpose</span>

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191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  |> c_pam leaves keep_string</span></span>

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192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  |> c_pam leaves (Bytes.to_string keep_string)</span></span>

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193

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

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194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff">   BA1.enum leaf_vec</span>

</pre>

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195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff">   |> Enum.map (Array.get leaf_arr %> rtrans)</span></pre>

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