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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mafft">Debian Med / mafft</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2">e8272592</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-12-07T18:22:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 7.475</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c7f071c90963ddde80c846db829a9a963045c56a">
core/Makefile
</a>
</li>
<li class="file-stats">
<a href="#c3ec324a54d4c6fba98645a9da2c853fa3fbcb80">
<span class="new-file">
+
core/filter.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#258fa17aad7d901a96eadf2211f449a5e4eb2ef9">
core/io.c
</a>
</li>
<li class="file-stats">
<a href="#bf392a27539c02d920458de76ae4ba00c5a3d6d0">
core/mafft.tmpl
</a>
</li>
<li class="file-stats">
<a href="#fb792f1c5a19dfe68974be08a96f0756ba949034">
core/mltaln.h
</a>
</li>
<li class="file-stats">
<a href="#93f296c20fdcfe44e5dd58f323ceeddf6c24e552">
core/pairlocalalign.c
</a>
</li>
<li class="file-stats">
<a href="#40ad2378dbd6c39182cb9a040f6e0f9a9f2e56a6">
core/replaceu.c
</a>
</li>
<li class="file-stats">
<a href="#f78a71af8bbf8cc2f6f313549d4da14bd3771359">
readme
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="c7f071c90963ddde80c846db829a9a963045c56a">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#c7f071c90963ddde80c846db829a9a963045c56a"><strong>core/Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +57,7 @@ STRIP = strip</td>
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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
57
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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC57" class="line" lang="make"><span class="nv" style="color: #008080;">PROGS</span> <span class="o" style="font-weight: 600;">=</span> dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign <span class="se" style="color: #d14;">\</span></span>
</pre>
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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">
58
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"> multi2hat3s pairash addsingle maffttext2hex hex2maffttext <span class="se" style="color: #d14;">\</span></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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"> splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
60
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<td class="diff-line-num new_line old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="make"> seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num new old_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">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="make"> seq2regtable regtable2seq score getlag dndpre setcore <span class="idiff left right">filter </span>replaceu restoreu setdirection makedirectionlist version <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="61" 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="61" 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">
61
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"> <span class="nv" style="color: #008080;">$(DASH_CLIENT)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="62" 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="62" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC62" class="line" lang="make"><span class="nv" style="color: #008080;">SOS</span> <span class="o" style="font-weight: 600;">=</span> libdisttbfast.so</span>
</pre>
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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">
63
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"><span class="nv" style="color: #008080;">DLLS</span> <span class="o" style="font-weight: 600;">=</span> libdisttbfast.dll</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" 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="66" 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">@@ -66,6 +66,7 @@ DYLIBS = libdisttbfast.dylib</td>
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<td class="diff-line-num old_line" data-linenumber="66" 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">
66
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<td class="diff-line-num new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"><span class="nv" style="color: #008080;">PERLPROGS</span> <span class="o" style="font-weight: 600;">=</span> mafftash_premafft.pl seekquencer_premafft.pl</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">
67
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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">
67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"><span class="nv" style="color: #008080;">SCRIPTS</span> <span class="o" style="font-weight: 600;">=</span> mafft mafft-homologs.rb mafft-sparsecore.rb</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="68" 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">
68
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<td class="diff-line-num new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"><span class="nv" style="color: #008080;">OBJSETDIRECTION</span> <span class="o" style="font-weight: 600;">=</span> mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="69" 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="69" 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="make"><span class="nv" style="color: #008080;">OBJFILTER</span> <span class="o" style="font-weight: 600;">=</span> mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o</span>
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<td class="diff-line-num old_line" data-linenumber="69" 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">
69
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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">
70
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"><span class="nv" style="color: #008080;">OBJREPLACEU</span> <span class="o" style="font-weight: 600;">=</span> mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o</span>
</pre>
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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">
70
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<td class="diff-line-num new_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">
71
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"><span class="nv" style="color: #008080;">OBJRESTOREU</span> <span class="o" style="font-weight: 600;">=</span> mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o</span>
</pre>
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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">
71
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC72" class="line" lang="make"><span class="nv" style="color: #008080;">OBJREGTABLE2SEQ</span> <span class="o" style="font-weight: 600;">=</span> mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" 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="162" 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">@@ -161,8 +162,9 @@ dylibs : $(DYLIBS)</td>
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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="make"><span class="nl">dlls </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(DLLS)</span></span>
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<td class="diff-line-num old_line" data-linenumber="162" 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="163" 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="LC163" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="make"><span class="nl">$(DASH_CLIENT)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">dash_client.go</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="make"> go build dash_client.go</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># go build --ldflags '-extldflags "-static"' dash_client.go</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># go build dash_client.go</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">env</span> <span class="nv" style="color: #008080;">CGO_ENABLED</span><span class="o" style="font-weight: 600;">=</span>0 go build <span class="nt" style="color: #000080;">--ldflags</span> <span class="s1" style="color: #d14;">'-extldflags "-static"'</span> dash_client.go <span class="c" style="color: #998; font-style: italic;"># for conda</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="make"><span class="nl">univscript</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">univscript.tmpl Makefile</span></span>
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168
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s:_PROGS:</span><span class="nv" style="color: #008080;">$(PROGS)</span><span class="s2" style="color: #d14;">:"</span> univscript.tmpl <span class="o" style="font-weight: 600;">></span> univscript</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="241" 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="243" 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">@@ -241,6 +243,9 @@ setdirection : $(OBJSETDIRECTION)</td>
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241
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="make"><span class="nl">replaceu </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJREPLACEU)</span></span>
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242
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$(OBJREPLACEU)</span> <span class="nv" style="color: #008080;">$(MYCFLAGS)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LIBS)</span></span>
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243
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="make"><span class="nl">filter </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJFILTER)</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$(OBJFILTER)</span> <span class="nv" style="color: #008080;">$(MYCFLAGS)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LIBS)</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="make"></span>
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244
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="make"><span class="nl">restoreu </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJRESTOREU)</span></span>
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245
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$(OBJRESTOREU)</span> <span class="nv" style="color: #008080;">$(MYCFLAGS)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LIBS)</span></span>
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246
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#c3ec324a54d4c6fba98645a9da2c853fa3fbcb80"><strong>core/filter.c</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mltaln.h"</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DEBUG 0</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxunusual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">count_unusual</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">usual</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pt</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"> <span class="n" style="color: #333;">pt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pt</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strchr</span><span class="p">(</span> <span class="n" style="color: #333;">usual</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pt</span> <span class="p">)</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"> <span class="n" style="color: #333;">pt</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "%d/%d=%f\n", count, pt-seq, ((double)count/(pt-seq)) );</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">arguments</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[]</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">maxunusual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">;</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">inputfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">dorp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NOTSPECIFIED</span><span class="p">;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">argv</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span> <span class="p">)</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="p">{</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="p">)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="p">)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">:</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">maxunusual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myatof</span><span class="p">(</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">argv</span> <span class="p">);</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxunusual = %f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">maxunusual</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">argc</span><span class="p">;</span></span>
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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="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">nextoption</span><span class="p">;</span></span>
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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="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">inputfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">argv</span><span class="p">;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "inputfile = %s\n", inputfile );</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">argc</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">nextoption</span><span class="p">;</span></span>
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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="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'D'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">dorp</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">;</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">dorp</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="nl">default:</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"illegal option %c</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">c</span> <span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="p">}</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="p">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="nl">nextoption:</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="p">;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="p">}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> </span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="p">{</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"options: Check source file !</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="p">}</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"><span class="p">}</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[]</span> <span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">infp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nlenmin</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nlen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">usual</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nout</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpseq</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">arguments</span><span class="p">(</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="p">);</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">inputfile</span> <span class="p">)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">infp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span> <span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span> <span class="p">);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">infp</span> <span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="p">{</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cannot open %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span> <span class="p">);</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="p">}</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="p">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">infp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdin</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// dorp = NOTSPECIFIED;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">getnumlen_casepreserve</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nlenmin</span> <span class="p">);</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">nlenmax</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">nlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">tmpseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateCharVec</span><span class="p">(</span> <span class="n" style="color: #333;">nlenmax</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// readData_pointer( infp, name, nlen, seq );</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">readData_pointer_casepreserve</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span> <span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span> <span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FILE *origfp;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> origfp = fopen( "_original", "w" );</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( !origfp )</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> fprintf( stderr, "Cannot open _original\n" );</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exit( 1 );</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> for( i=0; i<njob; i++ )</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> {</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> nlen[i] = strlen( seq[i] );</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> fprintf( origfp, ">%s\n", name[i]+1 );</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> fprintf( origfp, "%s\n", seq[i] );</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> fclose( origfp );</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dorp</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'p'</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">usual</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">usual</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ATGCUatgcu-"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">nout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">njob</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">gappick0</span><span class="p">(</span> <span class="n" style="color: #333;">tmpseq</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">count_unusual</span><span class="p">(</span> <span class="n" style="color: #333;">tmpseq</span><span class="p">,</span> <span class="n" style="color: #333;">usual</span> <span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxunusual</span> <span class="p">)</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">nout</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"></span>
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<td class="diff-line-num new new_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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">nout</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">njob</span> <span class="p">)</span></span>
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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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="p">{</span></span>
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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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">dorp</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'p'</span> <span class="p">)</span></span>
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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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Removed %d sequence(s) where the frequency of ambiguous amino acids > %5.3f</span><span class="se" style="color: #d14;">\n\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nout</span><span class="p">,</span> <span class="n" style="color: #333;">maxunusual</span> <span class="p">);</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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Removed %d sequence(s) where the frequency of ambiguous bases > %5.3f</span><span class="se" style="color: #d14;">\n\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nout</span><span class="p">,</span> <span class="n" style="color: #333;">maxunusual</span> <span class="p">);</span></span>
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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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="p">}</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> </span>
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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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">nlen</span> <span class="p">);</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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">tmpseq</span> <span class="p">);</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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span> <span class="p">);</span></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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">name</span> <span class="p">);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#258fa17aad7d901a96eadf2211f449a5e4eb2ef9"><strong>core/io.c</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">@@ -2664,7 +2664,9 @@ void readhat2_doublehalf_part_pointer( FILE *fp, int nseq, int nadd, char **name</td>
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<pre style="margin: 0;"> <span id="LC2664" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">B</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC2665" class="line" lang="c"></span>
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2666
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2666
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<pre style="margin: 0;"> <span id="LC2666" class="line" lang="c"> <span class="n" style="color: #333;">fgets</span><span class="p">(</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">B</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="p">);</span></span>
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2667
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<pre style="margin: 0;">-<span id="LC2667" class="line" lang="c"> <span class="n" style="color: #333;">fgets</span><span class="p">(</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">B</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="p">);</span> <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">nseq0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span> <span class="n" style="color: #333;">b</span> <span class="p">);</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">nseq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nseq0</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC2667" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) </span></span>
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2668
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<pre style="margin: 0;">+<span id="LC2668" class="line" lang="c"> <span class="n" style="color: #333;">fgets</span><span class="p">(</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">B</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="p">);</span> <span class="n" style="color: #333;">nseq0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span> <span class="n" style="color: #333;">b</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2020/Oct/23</span></span>
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<pre style="margin: 0;">+<span id="LC2669" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">nseq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nseq0</span> <span class="p">)</span> </span>
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2670
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<pre style="margin: 0;"> <span id="LC2670" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2671" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d != %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nseq</span><span class="p">,</span> <span class="n" style="color: #333;">nseq0</span> <span class="p">);</span></span>
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2670
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<pre style="margin: 0;"> <span id="LC2672" class="line" lang="c"> <span class="n" style="color: #333;">ErrorExit</span><span class="p">(</span> <span class="s" style="color: #d14;">"hat2 is wrong."</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#bf392a27539c02d920458de76ae4ba00c5a3d6d0"><strong>core/mafft.tmpl</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash </span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">er</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">myself</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span>/<span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>myself</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v7.47<span class="idiff left right">1 (2020/Jul/</span>3)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v7.47<span class="idiff left right">5 (2020/Nov/2</span>3)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">LANG</span><span class="o" style="font-weight: 600;">=</span>C<span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>LANG</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">os</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">uname</span><span class="sb" style="color: #d14;">`</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" 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="257" 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">@@ -257,6 +257,7 @@ laraparams="/dev/null"</td>
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257
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="shell"><span class="nv" style="color: #008080;">foldalignopt</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span></span>
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<td class="diff-line-num old_line" data-linenumber="258" 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">
258
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<td class="diff-line-num new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="shell"><span class="nv" style="color: #008080;">treealg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -X 0.1 "</span></span>
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<td class="diff-line-num old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="shell"><span class="nv" style="color: #008080;">sueff</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"1.0"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="shell"><span class="nv" style="color: #008080;">maxambiguous</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"1.0"</span></span>
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260
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<td class="diff-line-num new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="shell"><span class="nv" style="color: #008080;">scoreoutarg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span></span>
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<td class="diff-line-num old_line" data-linenumber="261" 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">
261
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="shell"><span class="nv" style="color: #008080;">numthreads</span><span class="o" style="font-weight: 600;">=</span>0</span>
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262
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="shell"><span class="nv" style="color: #008080;">numthreadsit</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="405" 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="406" 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">@@ -405,6 +406,9 @@ if [ $# -gt 0 ]; then</td>
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405
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">shift </span></span>
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406
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<td class="diff-line-num new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">sueff</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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407
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<td class="diff-line-num new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="shell"> <span class="nv" style="color: #008080;">treealg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -X </span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="408" 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="409" 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">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--maxambiguous"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="410" 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">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">shift </span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">maxambiguous</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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408
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<td class="diff-line-num new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--noscore"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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409
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<td class="diff-line-num new_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">scorecalcopt</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -Z "</span></span>
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410
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<td class="diff-line-num new_line" data-linenumber="414" 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">
414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"--6mermultipair"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1046,7 +1050,7 @@ function removetmpfile() { # for MPI</td>
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1046
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$debug</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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1047
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<td class="diff-line-num new_line" data-linenumber="1051" 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">
1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys</span></span>
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<td class="diff-line-num old_line" data-linenumber="1048" 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">
1048
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<td class="diff-line-num new_line" data-linenumber="1052" 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">
1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1049
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<td class="diff-line-num new_line old" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"tar cfv - </span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> | gzip -c > debuginfo.tgz; removetmpfile"</span> 0 15</span>
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<td class="diff-line-num new old_line" data-linenumber="1050" 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="1053" 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">
1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">popd > /dev/null 2>&1; </span>tar cfv - </span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> | gzip -c > debuginfo.tgz; removetmpfile"</span> 0 15</span>
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<td class="diff-line-num old_line" data-linenumber="1050" 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">
1050
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<td class="diff-line-num new_line" data-linenumber="1054" 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">
1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old_line" data-linenumber="1051" 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">
1051
</td>
<td class="diff-line-num new_line" data-linenumber="1055" 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">
1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># trap "rm -rf $TMPFILE" 0 15</span></span>
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<td class="diff-line-num old_line" data-linenumber="1052" 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">
1052
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<td class="diff-line-num new_line" data-linenumber="1056" 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">
1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"removetmpfile"</span> 0 15</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1065" 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="1069" 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">@@ -1065,8 +1069,16 @@ function removetmpfile() { # for MPI</td>
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<td class="diff-line-num old_line" data-linenumber="1065" 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">
1065
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<td class="diff-line-num new_line" data-linenumber="1069" 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">
1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1066" 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">
1066
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<td class="diff-line-num new_line" data-linenumber="1070" 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">
1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/infile"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1067" 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">
1067
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<td class="diff-line-num new_line" data-linenumber="1071" 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">
1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">>></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/infile"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1068
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<td class="diff-line-num new_line old" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1068" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$addfile</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="s2" style="color: #d14;">"^$"</span> <span class="o" style="font-weight: 600;">>></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/infile"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1069" 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">
1069
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<td class="diff-line-num new_line" data-linenumber="1072" 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">
1072
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1072" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$addfile</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="s2" style="color: #d14;">"^$"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_addfile"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$maxambiguous</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"1.0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1075" 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">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mv</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/infile"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_tofilter"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1076" 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">
1076
</td>
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/filter"</span> <span class="nt" style="color: #000080;">-m</span> <span class="nv" style="color: #008080;">$maxambiguous</span> <span class="nv" style="color: #008080;">$seqtype</span> <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_tofilter"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/infile"</span> 2>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="diff-line-num new new_line" data-linenumber="1077" 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">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_addfile"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_tofilter"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1078" 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">
1078
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1078" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/filter"</span> <span class="nt" style="color: #000080;">-m</span> <span class="nv" style="color: #008080;">$maxambiguous</span> <span class="nv" style="color: #008080;">$seqtype</span> <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_tofilter"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_addfile"</span> 2>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_addfile"</span> <span class="o" style="font-weight: 600;">>></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/infile"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1070" 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">
1070
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<td class="diff-line-num new_line" data-linenumber="1082" 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">
1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$scorematrix</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="s2" style="color: #d14;">"^$"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_aamtx"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1071
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<td class="diff-line-num new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$mergetable</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="s2" style="color: #d14;">"^$"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_subalignmentstable"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1072" 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">
1072
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<td class="diff-line-num new_line" data-linenumber="1084" 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">
1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$treeinfile</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="s2" style="color: #d14;">"^$"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_guidetree"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1190" 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="1202" 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">@@ -1190,7 +1202,9 @@ $ownlist"</td>
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<td class="diff-line-num old_line" data-linenumber="1190" 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">
1190
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<td class="diff-line-num new_line" data-linenumber="1202" 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">
1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1191" 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">
1191
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<td class="diff-line-num new_line" data-linenumber="1203" 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">
1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="1192" 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">
1192
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<td class="diff-line-num new_line" data-linenumber="1204" 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">
1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" data-linenumber="1193" 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="1205" 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">
1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1193" 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">
1193
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<td class="diff-line-num new_line" data-linenumber="1206" 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">
1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$addarg0</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1194" 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="1207" 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">
1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1194" 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">
1194
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<td class="diff-line-num new_line" data-linenumber="1208" 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">
1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># iterate=0 # 2013/03/23 -> commented out, 2017/12</span></span>
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<td class="diff-line-num old_line" data-linenumber="1195" 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">
1195
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<td class="diff-line-num new_line" data-linenumber="1209" 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">
1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/countlen"</span> < <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/_addfile"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/addsize"</span> 2>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1196" 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">
1196
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<td class="diff-line-num new_line" data-linenumber="1210" 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">
1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="shell"> <span class="nv" style="color: #008080;">nadd</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print $1}'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMPFILE</span><span class="s2" style="color: #d14;">/addsize"</span><span class="sb" style="color: #d14;">`</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1305" 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="1319" 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">@@ -1305,6 +1319,13 @@ $ownlist"</td>
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<td class="diff-line-num old_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1305
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<td class="diff-line-num new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"npair = "</span> <span class="nv" style="color: #008080;">$npair</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1306
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<td class="diff-line-num new_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"nseq = "</span> <span class="nv" style="color: #008080;">$nseq</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1307
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<td class="diff-line-num new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"nlen = "</span> <span class="nv" style="color: #008080;">$nlen</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$norg</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1308" 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="1324" 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">
1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The reference sequence was removed because of ambiguous letters?"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1326" 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">
1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1327" 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">
1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1328" 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">
1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1308" 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">
1308
</td>
<td class="diff-line-num new_line" data-linenumber="1329" 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">
1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># nagasa check!</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1309" 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">
1309
</td>
<td class="diff-line-num new_line" data-linenumber="1330" 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">
1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1310" 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">
1310
</td>
<td class="diff-line-num new_line" data-linenumber="1331" 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">
1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$npair</span> <span class="nt" style="color: #000080;">-gt</span> 10000000 <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$nlen</span> <span class="nt" style="color: #000080;">-gt</span> 5000 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># 2017/Oct </span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1327" 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="1348" 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">@@ -1327,6 +1348,11 @@ $ownlist"</td>
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<td class="diff-line-num old_line" data-linenumber="1327" 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">
1327
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<td class="diff-line-num new_line" data-linenumber="1348" 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">
1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1328" 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">
1328
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<td class="diff-line-num new_line" data-linenumber="1349" 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">
1349
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1349" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1329" 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">
1329
</td>
<td class="diff-line-num new_line" data-linenumber="1350" 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">
1350
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1351" 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">
1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">awk</span> <span class="s2" style="color: #d14;">"BEGIN {print( 0.0+</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$maxambiguous</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> < 0.0 || 0.0+</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$maxambiguous</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> > 1.0 )}"</span><span class="sb" style="color: #d14;">`</span> <span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1352
</td>
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"The argument of --maxambiguous must be between 0.0 and 1.0"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1353" 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">
1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1354" 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">
1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1355" 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">
1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1330" 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">
1330
</td>
<td class="diff-line-num new_line" data-linenumber="1356" 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">
1356
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1356" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$allowshift</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1331
</td>
<td class="diff-line-num new_line" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1357
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1357" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$unalignspecified</span> <span class="nt" style="color: #000080;">-ne</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1332" 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">
1332
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<td class="diff-line-num new_line" data-linenumber="1358" 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">
1358
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">unalignlevel</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"0.8"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1945" 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="1971" 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">@@ -1945,6 +1971,7 @@ $ownlist"</td>
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1945
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<td class="diff-line-num new_line" data-linenumber="1971" 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">
1971
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<pre style="margin: 0;"> <span id="LC1971" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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1946
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1972
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<pre style="margin: 0;"> <span id="LC1972" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1947" 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">
1947
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1973
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<pre style="margin: 0;"> <span id="LC1973" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" data-linenumber="1948" 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="1974" 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">
1974
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<pre style="margin: 0;">+<span id="LC1974" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1948" 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">
1948
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1975
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<pre style="margin: 0;"> <span id="LC1975" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$nadd</span> <span class="nt" style="color: #000080;">-gt</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old_line" data-linenumber="1949" 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">
1949
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<td class="diff-line-num new_line" data-linenumber="1976" 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">
1976
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<pre style="margin: 0;"> <span id="LC1976" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$fragment</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1950
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<td class="diff-line-num new_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1977
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<pre style="margin: 0;"> <span id="LC1977" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">addarg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$addarg0</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$nadd</span><span class="s2" style="color: #d14;"> -g -0.01"</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1972" 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="1999" 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">@@ -1972,12 +1999,13 @@ $ownlist"</td>
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<td class="diff-line-num old_line" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1972
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<td class="diff-line-num new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1999
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<pre style="margin: 0;"> <span id="LC1999" class="line" lang="shell"> <span class="nv" style="color: #008080;">bunkatsuopt</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -B "</span> <span class="c" style="color: #998; font-style: italic;"># fftnsi demo bunktasu shinai</span></span>
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<td class="diff-line-num old_line" data-linenumber="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1973
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<td class="diff-line-num new_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$add2ndhalfarg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1974" 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">
1974
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<td class="diff-line-num new_line" data-linenumber="2001" 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">
2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$auto</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$iterate</span> <span class="nt" style="color: #000080;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1975" 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">
1975
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<pre style="margin: 0;">-<span id="LC1975" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">''</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1976
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<td class="diff-line-num new_line old" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1976" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'The --keeplength and --mapout options are not supported'</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1977" 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">
1977
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<td class="diff-line-num new_line old" data-linenumber="2002" 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="LC1977" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'with the --auto or --maxiterate >0 options.'</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1978
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<td class="diff-line-num new_line old" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1978" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Use the --maxiterate 0 option (= progressive method).'</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1979" 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">
1979
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<td class="diff-line-num new_line old" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC1979" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">''</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1980
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<td class="diff-line-num new_line old" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1980" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="diff-line-num new old_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2002
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<pre style="margin: 0;">+<span id="LC2002" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo '' 1>>"$progressfile"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2003" 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">
2003
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<pre style="margin: 0;">+<span id="LC2003" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2004
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2004" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"</span></span>
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2005
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<pre style="margin: 0;">+<span id="LC2005" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"</span></span>
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2006
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<pre style="margin: 0;">+<span id="LC2006" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo '' 1>>"$progressfile"</span></span>
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2007
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<pre style="margin: 0;">+<span id="LC2007" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># exit 1</span></span>
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2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="shell"> <span class="nv" style="color: #008080;">iterate</span><span class="o" style="font-weight: 600;">=</span>0</span>
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1981
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2009
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<pre style="margin: 0;"> <span id="LC2009" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1982
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<td class="diff-line-num new_line" data-linenumber="2010" 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">
2010
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<pre style="margin: 0;"> <span id="LC2010" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="1983" 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">
1983
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<td class="diff-line-num new_line" data-linenumber="2011" 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">
2011
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<pre style="margin: 0;"> <span id="LC2011" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2179" 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="2207" 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">@@ -2179,6 +2207,7 @@ $ownlist"</td>
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2179
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<td class="diff-line-num new_line" data-linenumber="2207" 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">
2207
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<pre style="margin: 0;"> <span id="LC2207" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "iterate = " $iterate 1>>"$progressfile"</span></span>
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2180
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<td class="diff-line-num new_line" data-linenumber="2208" 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">
2208
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<pre style="margin: 0;"> <span id="LC2208" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "cycle = " $cycle 1>>"$progressfile"</span></span>
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2181
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2209
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<pre style="margin: 0;"> <span id="LC2209" class="line" lang="shell"></span>
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2210
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<pre style="margin: 0;">+<span id="LC2210" class="line" lang="shell"></span>
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2182
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2211
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<pre style="margin: 0;"> <span id="LC2211" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$anysymbol</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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2183
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2212
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<pre style="margin: 0;"> <span id="LC2212" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mv </span>infile orig</span>
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2184
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2213
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<pre style="margin: 0;"> <span id="LC2213" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/replaceu"</span> <span class="nv" style="color: #008080;">$seqtype</span> <span class="nt" style="color: #000080;">-i</span> orig <span class="o" style="font-weight: 600;">></span> infile 2>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#fb792f1c5a19dfe68974be08a96f0756ba949034"><strong>core/mltaln.h</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">@@ -36,7 +36,7 @@</td>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.47<span class="idiff left right">1</span>"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.47<span class="idiff left right">5</span>"</span></span>
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40
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )</span></span>
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41
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FFT_THRESHOLD 80</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#93f296c20fdcfe44e5dd58f323ceeddf6c24e552"><strong>core/pairlocalalign.c</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">@@ -2475,7 +2475,8 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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<pre style="margin: 0;"> <span id="LC2475" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">ngui</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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2476
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2476
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<pre style="margin: 0;"> <span id="LC2476" class="line" lang="c"> <span class="p">{</span></span>
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2477
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2477
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<pre style="margin: 0;"> <span id="LC2477" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'Y'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'r'</span> <span class="p">)</span></span>
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2478
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<pre style="margin: 0;">-<span id="LC2478" class="line" lang="c"> <span class="n" style="color: #333;">distancemtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="p">,</span> <span class="n" style="color: #333;">nadd</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2478" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// distancemtx = AllocateDoubleMtx( njob, nadd );</span></span>
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<pre style="margin: 0;">+<span id="LC2479" class="line" lang="c"> <span class="n" style="color: #333;">distancemtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nadd</span><span class="p">,</span> <span class="n" style="color: #333;">nadd</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2020/Oct/23</span></span>
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2480
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<pre style="margin: 0;"> <span id="LC2480" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2481
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<pre style="margin: 0;"> <span id="LC2481" class="line" lang="c"> <span class="n" style="color: #333;">distancemtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateDoubleHalfMtx</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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2482
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<pre style="margin: 0;"> <span id="LC2482" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// distancemtx = AllocateDoubleMtx( njob, njob );</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3051" 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="3052" 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">@@ -3051,7 +3052,13 @@ static void pairalign( char **name, int *nlen, char **seq, char **aseq, char **d</td>
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3051
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<pre style="margin: 0;"> <span id="LC3052" class="line" lang="c"> <span class="p">}</span></span>
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3053
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<pre style="margin: 0;"> <span id="LC3053" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">distseq1</span> <span class="p">);</span></span>
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3054
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<pre style="margin: 0;"> <span id="LC3054" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">distseq2</span> <span class="p">);</span></span>
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3054
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<pre style="margin: 0;">-<span id="LC3054" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">store_dist</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ngui</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">FreeDoubleHalfMtx</span><span class="p">(</span> <span class="n" style="color: #333;">distancemtx</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3055" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">store_dist</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ngui</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC3056" class="line" lang="c"> <span class="p">{</span></span>
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3057
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<pre style="margin: 0;">+<span id="LC3057" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'Y'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">alg</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'r'</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3058" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleMtx</span><span class="p">(</span> <span class="n" style="color: #333;">distancemtx</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 2020/Oct/23</span></span>
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<pre style="margin: 0;">+<span id="LC3059" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC3060" class="line" lang="c"> <span class="n" style="color: #333;">FreeDoubleHalfMtx</span><span class="p">(</span> <span class="n" style="color: #333;">distancemtx</span><span class="p">,</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3061" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3062" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC3063" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">targetmap</span> <span class="p">);</span></span>
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3064
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<pre style="margin: 0;"> <span id="LC3064" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">targetmapr</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#40ad2378dbd6c39182cb9a040f6e0f9a9f2e56a6"><strong>core/replaceu.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="104" 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">@@ -104,6 +104,7 @@ int main( int argc, char *argv[] )</td>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">nlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocateIntVec</span><span class="p">(</span> <span class="n" style="color: #333;">njob</span> <span class="p">);</span></span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">readData_pointer_casepreserve</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">nlen</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span> <span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span> <span class="n" style="color: #333;">infp</span> <span class="p">);</span></span>
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107
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/e8272592c5f6005900af6cac62dd099793d19be2#f78a71af8bbf8cc2f6f313549d4da14bd3771359"><strong>readme</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">-----------------------------------------------------------------------</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> MAFFT: a multiple sequence alignment program</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> version 7.47<span class="idiff left right">1, 2020/Jul/</span>3</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> version 7.47<span class="idiff left right">5, 2020/Nov/2</span>3</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> http://mafft.cbrc.jp/alignment/software/</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> katoh@ifrec.osaka-u.ac.jp</span>
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