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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/207670d8e2ae7eb679e03ca85b51ac34a622902e">207670d8</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-15T13:14:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 7.467</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#171cea6c847639ec6a600b2378fe99ff36078c30">
core/Falign.c
</a>
</li>
<li class="file-stats">
<a href="#24411c4bd5a7db0f54552bf0091c326e97320448">
core/addsingle.c
</a>
</li>
<li class="file-stats">
<a href="#e74042ece92eca0b9cf69f319f6a4154e71044b9">
core/defs.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>
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<li class="file-stats">
<a href="#f78a71af8bbf8cc2f6f313549d4da14bd3771359">
readme
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</li>
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<h4>Changes:</h4>
<li id="171cea6c847639ec6a600b2378fe99ff36078c30">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/207670d8e2ae7eb679e03ca85b51ac34a622902e#171cea6c847639ec6a600b2378fe99ff36078c30"><strong>core/Falign.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1364" style="width: 35px; color: rgba(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">@@ -1364,6 +1364,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );</td>
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<td class="diff-line-num old_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1364
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<td class="diff-line-num new_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">clus2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span> <span class="n" style="color: #333;">result2</span><span class="p">[</span><span class="n" style="color: #333;">j</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1365
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<td class="diff-line-num new_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1365
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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="c"> <span class="n" style="color: #333;">totalscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1366
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1366
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fftlog</span> <span class="o" style="font-weight: 600;">=</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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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nin Falign(), *fftlog = %d\n", *fftlog );</span></span>
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1367
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<td class="diff-line-num new_line" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1368
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<pre style="margin: 0;"> <span id="LC1368" 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;">count</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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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1368
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<td class="diff-line-num new_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="c"> <span class="p">{</span></span>
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1369
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<td class="diff-line-num new_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fftlog</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 unfold js-unfold old_line" data-linenumber="1580" style="width: 35px; color: rgba(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="1581" style="width: 35px; color: rgba(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">@@ -1580,6 +1581,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );</td>
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1580
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1581
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<pre style="margin: 0;"> <span id="LC1581" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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1581
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<td class="diff-line-num new_line" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1582
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<pre style="margin: 0;"> <span id="LC1582" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<td class="diff-line-num new_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1583
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<pre style="margin: 0;"> <span id="LC1583" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1584" 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">
1584
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<pre style="margin: 0;">+<span id="LC1584" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nafter Falign(), *fftlog = %d\n", *fftlog );</span></span>
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1583
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<td class="diff-line-num new_line" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1585
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<pre style="margin: 0;"> <span id="LC1585" class="line" lang="c"></span>
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1584
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1586
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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if KEIKA</span></span>
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1585
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1587
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<pre style="margin: 0;"> <span id="LC1587" 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;">"DP ... done </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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3402" style="width: 35px; color: rgba(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="3404" style="width: 35px; color: rgba(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">@@ -3402,6 +3404,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );</td>
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3402
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3404
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<pre style="margin: 0;"> <span id="LC3404" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">clus2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span> <span class="n" style="color: #333;">result2</span><span class="p">[</span><span class="n" style="color: #333;">j</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3403
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3405
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<pre style="margin: 0;"> <span id="LC3405" class="line" lang="c"> <span class="n" style="color: #333;">totalscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3404
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3406
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<pre style="margin: 0;"> <span id="LC3406" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fftlog</span> <span class="o" style="font-weight: 600;">=</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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3407
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<pre style="margin: 0;">+<span id="LC3407" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nin Falign_udpari(), *fftlog = %d\n", *fftlog );</span></span>
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3405
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3408
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<pre style="margin: 0;"> <span id="LC3408" 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;">count</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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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3409
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<pre style="margin: 0;"> <span id="LC3409" class="line" lang="c"> <span class="p">{</span></span>
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3407
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3410
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<pre style="margin: 0;"> <span id="LC3410" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fftlog</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 unfold js-unfold new_line" data-linenumber="3552" style="width: 35px; color: rgba(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">@@ -3549,6 +3552,10 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );</td>
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3549
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3552
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<pre style="margin: 0;"> <span id="LC3552" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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3550
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3553
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<pre style="margin: 0;"> <span id="LC3553" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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3551
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3554
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<pre style="margin: 0;"> <span id="LC3554" class="line" lang="c"> <span class="p">}</span></span>
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3555
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<pre style="margin: 0;">+<span id="LC3555" class="line" lang="c"></span>
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3556
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<pre style="margin: 0;">+<span id="LC3556" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC3557" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// reporterr( "\nafter Falign_udpari(), *fftlog = %d\n", *fftlog );</span></span>
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3558
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<pre style="margin: 0;">+<span id="LC3558" class="line" lang="c"></span>
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3552
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3559
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<pre style="margin: 0;"> <span id="LC3559" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if KEIKA</span></span>
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3553
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3560
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<pre style="margin: 0;"> <span id="LC3560" 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;">"DP ... done </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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3554
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3561
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<pre style="margin: 0;"> <span id="LC3561" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/207670d8e2ae7eb679e03ca85b51ac34a622902e#24411c4bd5a7db0f54552bf0091c326e97320448"><strong>core/addsingle.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">@@ -1389,7 +1389,8 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo</td>
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1389
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<pre style="margin: 0;"> <span id="LC1389" class="line" lang="c"></span>
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1390
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="c"></span>
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1391
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1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );</span></span>
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1392
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<pre style="margin: 0;">-<span id="LC1392" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="p">)</span> <span class="n" style="color: #333;">ffttry</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1000</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">clus2</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1000</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );</span></span>
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fftlog</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="p">)</span> <span class="n" style="color: #333;">ffttry</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clus1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nlen</span><span class="p">[</span><span class="n" style="color: #333;">m2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clus2</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ffttry</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="LC1395" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708</span></span>
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (double)len1/fftlog[m1], clus1, (double)len2/fftlog[m2], clus2 );</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2961,7 +2962,7 @@ int main( int argc, char *argv[] )</td>
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2962
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<pre style="margin: 0;"> <span id="LC2962" 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;">"norg = %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;">norg</span> <span class="p">);</span></span>
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2962
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2963
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<pre style="margin: 0;"> <span id="LC2963" 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;">"njobc = %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;">njobc</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2964" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// if( norg > 1000 || nadd > 1000 ) use_fft = 0;</span></span>
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<pre style="margin: 0;">-<span id="LC2964" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">norg</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1000</span> <span class="p">)</span> <span class="n" style="color: #333;">use_fft</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="LC2965" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span> if( norg > 1000 ) use_fft = 0;</span></span>
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<pre style="margin: 0;"> <span id="LC2966" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2967" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2968" class="line" lang="c"> <span class="n" style="color: #333;">fullseqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alloclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nlenmax</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//chuui!</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/207670d8e2ae7eb679e03ca85b51ac34a622902e#e74042ece92eca0b9cf69f319f6a4154e71044b9"><strong>core/defs.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 class="cp" style="color: #999; font-weight: 600;">#include "dp.h"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TLS</span></span> <span class="n" style="color: #333;">commonAlloc1</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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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TLS</span></span> <span class="n" style="color: #333;">commonAlloc2</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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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TLS</span></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">commonIP</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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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TLS</span></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">commonJP</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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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">TLS</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">commonAlloc1</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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">TLS</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">commonAlloc2</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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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">TLS</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">commonIP</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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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">TLS</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">commonJP</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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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nthread</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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9
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9
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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;">nthreadpair</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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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">randomseed</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 unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(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="115" style="width: 35px; color: rgba(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">@@ -115,7 +115,7 @@ double consweight_multi = 1.0;</td>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">consweight_rna</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">RNAscoremtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">;</span></span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TLS</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">newgapstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">TLS</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">char</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">newgapstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>
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119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"></span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nalphabets</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">26</span><span class="p">;</span></span>
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121
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nscoredalphabets</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span></span>
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1
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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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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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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;">"v7.46<span class="idiff left right">4 (2020/Apr/21</span>)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">"v7.46<span class="idiff left right">7 (2020/May/14</span>)"</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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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<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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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2316,11 +2316,8 @@ function removetmpfile() { # for MPI</td>
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2316
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2316
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<pre style="margin: 0;"> <span id="LC2316" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2317
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<td class="diff-line-num new_line" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2317
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<pre style="margin: 0;"> <span id="LC2317" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$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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2318
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2318
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mv </span>orig infile <span class="c" style="color: #998; font-style: italic;"># replaceu wo mukouka</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2319" 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">
2319
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<td class="diff-line-num new_line old" data-linenumber="2319" 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="LC2319" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#else</span></span>
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2320
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<td class="diff-line-num new_line old" data-linenumber="2319" 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="LC2320" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Check sequence here</span></span>
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2321
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2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2322
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<pre style="margin: 0;">-<span id="LC2322" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mv infile infile2</span></span>
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2323
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<pre style="margin: 0;">-<span id="LC2323" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat /dev/null > infile</span></span>
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2320
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<pre style="margin: 0;">+<span id="LC2320" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/-//g'</span> infile <span class="o" style="font-weight: 600;">></span> dashin <span class="c" style="color: #998; font-style: italic;"># gap nozoku</span></span>
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2324
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2321
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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2325
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2322
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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="nt" style="color: #000080;">-o</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</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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2326
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2323
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<pre style="margin: 0;"> <span id="LC2323" 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>&2</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2335" style="width: 35px; color: rgba(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="2332" style="width: 35px; color: rgba(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">@@ -2335,7 +2332,7 @@ function removetmpfile() { # for MPI</td>
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2335
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2332
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<pre style="margin: 0;"> <span id="LC2332" 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="2336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2336
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2333
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<pre style="margin: 0;"> <span id="LC2333" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<td class="diff-line-num old_line" data-linenumber="2337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2337
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<td class="diff-line-num new_line" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2334
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<pre style="margin: 0;"> <span id="LC2334" 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;">"Calling DASH (https://sysimm.org/dash/)"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2338
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<pre style="margin: 0;">-<span id="LC2338" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="nt" style="color: #000080;">-i</span> <span class="idiff left right">infile</span> <span class="nt" style="color: #000080;">-sequences</span> dashsequences <span class="nt" style="color: #000080;">-hat3</span> hat3.seed 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2335
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<pre style="margin: 0;">+<span id="LC2335" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/dash_client"</span> <span class="nt" style="color: #000080;">-i</span> <span class="idiff left right">dashin</span> <span class="nt" style="color: #000080;">-sequences</span> dashsequences <span class="nt" style="color: #000080;">-hat3</span> hat3.seed 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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2339
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2336
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<pre style="margin: 0;"> <span id="LC2336" class="line" lang="shell"> <span class="nv" style="color: #008080;">dashres</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$?</span><span class="s2" style="color: #d14;">"</span></span>
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2340
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2337
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<pre style="margin: 0;"> <span id="LC2337" 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;">$dashres</span> <span class="nt" style="color: #000080;">-ne</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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2341
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2338
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<pre style="margin: 0;"> <span id="LC2338" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Error in DASH"</span> 1>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span></span>
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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">@@ -2348,6 +2345,17 @@ function removetmpfile() { # for MPI</td>
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2348
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2345
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<pre style="margin: 0;"> <span id="LC2345" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>ho_excluded dashsequences</span>
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2349
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2346
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<pre style="margin: 0;"> <span id="LC2346" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2350
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2347
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<pre style="margin: 0;"> <span id="LC2347" class="line" lang="shell"></span>
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2348
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<pre style="margin: 0;">+<span id="LC2348" 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;">$mergetable</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"/dev/null"</span> <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;"># 2020/Apr/30</span></span>
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2349
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<pre style="margin: 0;">+<span id="LC2349" class="line" lang="shell"> <span class="nv" style="color: #008080;">ndash</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'>DASH_'</span> dashsequences | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span><span class="sb" style="color: #d14;">`</span></span>
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2350
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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "ndash = " $ndash</span></span>
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2351
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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s2" style="color: #d14;">"{for( i=1;i<=NF;i++){if(0+</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">i==0)break; printf( </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">%d </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">, </span><span class="nv" style="color: #008080;">$ndash</span><span class="s2" style="color: #d14;">+</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">i); } print </span><span class="se" style="color: #d14;">\"\"</span><span class="s2" style="color: #d14;"> }"</span> _subalignmentstable <span class="o" style="font-weight: 600;">></span> _subalignmentstableshifted</span>
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2352
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<pre style="margin: 0;">+<span id="LC2352" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>_subalignmentstableshifted _subalignmentstable</span>
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2353
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<pre style="margin: 0;">+<span id="LC2353" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp </span>dashsequences dashsequences.bk</span>
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2354
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<pre style="margin: 0;">+<span id="LC2354" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s2" style="color: #d14;">"BEGIN{nout=0} {if(</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">1~/^>/) nout++; if( nout <= </span><span class="nv" style="color: #008080;">$ndash</span><span class="s2" style="color: #d14;"> ) print;}"</span> dashsequences <span class="o" style="font-weight: 600;">></span> infile2</span>
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2355
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<pre style="margin: 0;">+<span id="LC2355" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat </span>infile <span class="o" style="font-weight: 600;">>></span> infile2</span>
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2356
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp </span>infile2 dashsequences</span>
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2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2358
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<pre style="margin: 0;">+<span id="LC2358" class="line" lang="shell"></span>
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2351
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2359
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<pre style="margin: 0;"> <span id="LC2359" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/>DASH_/>DASH|/'</span> dashsequences <span class="o" style="font-weight: 600;">></span> renamed</span>
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2352
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2360
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<pre style="margin: 0;"> <span id="LC2360" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>renamed dashsequences</span>
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2353
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2361
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Done."</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2366" style="width: 35px; color: rgba(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="2374" style="width: 35px; color: rgba(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">@@ -2366,54 +2374,11 @@ function removetmpfile() { # for MPI</td>
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2366
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<td class="diff-line-num new_line" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2374
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<pre style="margin: 0;"> <span id="LC2374" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat </span>dashsequences <span class="o" style="font-weight: 600;">></span> infile</span>
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<td class="diff-line-num old_line" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2367
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<td class="diff-line-num new_line" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2375
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<pre style="margin: 0;"> <span id="LC2375" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat infile2 >> infile</span></span>
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2368
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<td class="diff-line-num new_line" data-linenumber="2376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2376
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<pre style="margin: 0;"> <span id="LC2376" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2369" 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">
2369
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2369" class="line" lang="shell"></span>
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2370
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2370" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># elif [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2371" 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">
2371
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2371" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mv infile infile2</span></span>
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2372
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2372" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if [ $anysymbol -eq 1 ]; then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2373" 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">
2373
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2373" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mv orig orig2</span></span>
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2374
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2374" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat /dev/null > orig</span></span>
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2375
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2375" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>
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2376
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<pre style="margin: 0;">-<span id="LC2376" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat /dev/null > infile</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2377" 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">
2377
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2377" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2378" 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">
2378
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2378" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "strdir = " 1>>"$progressfile"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2379" 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">
2379
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2379" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo $strdir 1>>"$progressfile"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2380" 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">
2380
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2380" 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 old_line" data-linenumber="2381" 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">
2381
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2381" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Calling DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/)" 1>>"$progressfile"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2382
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<td class="diff-line-num new_line old" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2382" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># perl "$prefix/mafftash_premafft.pl" -p pdblist -o ownlist -d "$strdir" 2>>"dasherr"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2383
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<td class="diff-line-num new_line old" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2383" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># dashres="$?"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2384" 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">
2384
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2384" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat dasherr 1>>"$progressfile"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2385" 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">
2385
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2385" 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 old_line" data-linenumber="2386" 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">
2386
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2386" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if [ $dashres -ne "0" ]; then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2387
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<td class="diff-line-num new_line old" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2387" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Error in DASH" 1>>"$progressfile"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2388" 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">
2388
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2388" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># exit 1;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2389" 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">
2389
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2389" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2390" 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">
2390
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<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2390" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Done." 1>>"$progressfile"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2391" 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">
2391
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2391" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2392" 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">
2392
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2392" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># seedoffset=`grep -c '^[>|=]' instr | head -1 ` </span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2393" 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">
2393
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2393" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2394" 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">
2394
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2394" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "# of structures = " 1>>"$progressfile"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2395" 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">
2395
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2395" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo $seedoffset 1>>"$progressfile"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2396" 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">
2396
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2396" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mv hat3 hat3.seed</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2397" 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">
2397
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2397" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2398" 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">
2398
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2398" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if [ $anysymbol -eq 1 ]; then</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2399
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC2399" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat instr >> orig</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2400
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2400" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># "$prefix/replaceu" $seqtype -i instr -o 0 > clean 2>>"$progressfile" || exit 1</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2401" 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">
2401
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2401" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mv clean infile</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2402" 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">
2402
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2402" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2403" 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">
2403
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2403" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2404" 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">
2404
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2404" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat orig2 >> orig</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2405" 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">
2405
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2405" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># else</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2406" 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">
2406
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2406" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat instr > infile</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2407" 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">
2407
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2407" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat infile2 >> infile</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2408" 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">
2408
</td>
<td class="diff-line-num new_line old" data-linenumber="2377" 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="LC2408" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2409
</td>
<td class="diff-line-num new_line" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2377
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2377" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2410
</td>
<td class="diff-line-num new_line" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2378
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2378" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> /dev/null <span class="o" style="font-weight: 600;">></span> hat3.seed</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2411
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<td class="diff-line-num new_line" data-linenumber="2379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2379
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<pre style="margin: 0;"> <span id="LC2379" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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2412
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2380
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<pre style="margin: 0;"> <span id="LC2380" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cat hat3.seed</span></span>
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2413
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2381
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<pre style="margin: 0;"> <span id="LC2381" class="line" lang="shell"></span>
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2414
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<pre style="margin: 0;">-<span id="LC2414" class="line" lang="shell"></span>
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2415
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<pre style="margin: 0;">-<span id="LC2415" class="line" lang="shell"></span>
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2416
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<pre style="margin: 0;">-<span id="LC2416" class="line" lang="shell"></span>
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2417
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2382
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<pre style="margin: 0;"> <span id="LC2382" 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;">$mccaskill</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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2418
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2383
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<pre style="margin: 0;"> <span id="LC2383" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">/mccaskillwrap"</span> <span class="nt" style="color: #000080;">-s</span> <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">$numthreads</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$prefix</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-i</span> infile <span class="o" style="font-weight: 600;">></span> hat4 2>><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$progressfile</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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2419
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2384
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<pre style="margin: 0;"> <span id="LC2384" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$dafs</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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<li id="fb792f1c5a19dfe68974be08a96f0756ba949034">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/207670d8e2ae7eb679e03ca85b51ac34a622902e#fb792f1c5a19dfe68974be08a96f0756ba949034"><strong>core/mltaln.h</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;">#define USE_XCED 0</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="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 _SVID_SOURCE</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _BSD_SOURCE</span></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 _XOPEN_SOURCE</span></span>
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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="cp" style="color: #999; font-weight: 600;">#if USE_XCED</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +36,7 @@</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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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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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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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 VERSION "7.46<span class="idiff left right">4</span>"</span></span>
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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 "7.46<span class="idiff left right">7</span>"</span></span>
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41
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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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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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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/207670d8e2ae7eb679e03ca85b51ac34a622902e#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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> MAFFT: a multiple sequence alignment program</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> version 7.46<span class="idiff left right">4, 2020/Apr/21</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> version 7.46<span class="idiff left right">7, 2020/May/14</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> katoh@ifrec.osaka-u.ac.jp</span>
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