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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741">01c9ee8d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-19T06:26:27Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5+dfsg</pre>

</li>

</ul>

<h4>12 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

.gitignore

</a>

</li>

<li class="file-stats">

<a href="#8d7bbc73f7c3ab1ec74d66a4a7dbc068df7f549e">

include/external_libs.h

</a>

</li>

<li class="file-stats">

<a href="#f13ce0fdb19229f1f614704114e03a5413980d10">

include/misc.h

</a>

</li>

<li class="file-stats">

<a href="#65ace6fbb909982bfbe2929205b5b57b8ea7ca19">

src/lib/base/matrix.c

</a>

</li>

<li class="file-stats">

<a href="#120416c598d701c4240159523284871a18a896d7">

src/lib/msa/maf.c

</a>

</li>

<li class="file-stats">

<a href="#440b536fb9362a7a47baa54729f4b22d199d332d">

src/lib/msa/maf_block.c

</a>

</li>

<li class="file-stats">

<a href="#d531898f3bec32e2718f0bdc23f7a294fbabc041">

src/lib/msa/sufficient_stats.c

</a>

</li>

<li class="file-stats">

<a href="#e000079933b4c58bf725cd26e5d22c166063d58c">

src/make-include.mk

</a>

</li>

<li class="file-stats">

<a href="#cbef062acd6c7d49ab15921df473b83bd2b10c07">

src/util/clean_genes.c

</a>

</li>

<li class="file-stats">

<a href="#53f2934d07552d00f50907ed7dce7be0e031c466">

src/util/msa_view.c

</a>

</li>

<li class="file-stats">

<a href="#0c4b050bc0a22bd9db927801a888e21a58e2721d">

test/test_phast.sh

</a>

</li>

<li class="file-stats">

<a href="#c692273deb2772da307ffe37041fef77bf4baa97">

version

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*.a</span>

</pre>

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2

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

</pre>

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3

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

</pre>

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4

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

</pre>

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5

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

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">doc/man/</span>

</pre>

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7

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

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<br>

</li>

<li id="8d7bbc73f7c3ab1ec74d66a4a7dbc068df7f549e">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#8d7bbc73f7c3ab1ec74d66a4a7dbc068df7f549e"><strong>include/external_libs.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,7 @@</td>

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33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

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34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VECLIB</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="36" 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="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <<span class="idiff left right">vecLib/clapack</span>.h></span></span>

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<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <<span class="idiff left right">Accelerate/Accelerate</span>.h></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define LAPACK_INT __CLPK_integer</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define LAPACK_DOUBLE __CLPK_doublereal</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

</td>

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<br>

</li>

<li id="f13ce0fdb19229f1f614704114e03a5413980d10">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#f13ce0fdb19229f1f614704114e03a5413980d10"><strong>include/misc.h</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,6 +87,17 @@ int int_pow(int x, int y) {</td>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">retval</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Take x,y & max as int and cast x & y as double</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *  * raise x to the power y. return min(x^y,max) as int*/</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">PHAST_INLINE</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">pow_bounded</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"><span class="p">}</span></span>

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

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

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

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** \name Log based calculation functions</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">\{ */</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"></span>

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<br>

</li>

<li id="65ace6fbb909982bfbe2929205b5b57b8ea7ca19">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#65ace6fbb909982bfbe2929205b5b57b8ea7ca19"><strong>src/lib/base/matrix.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" style="width: 35px; color: rgba(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="293" style="width: 35px; color: rgba(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">@@ -293,7 +293,8 @@ int mat_invert(Matrix *M_inv, Matrix *M) {</td>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   same dimension, and C is diagonal.  C is described by a vector</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   representing its diagonal elements.  */</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mat_mult_diag</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">B</span><span class="p">,</span> <span class="n" style="color: #333;">Vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">C</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*  int i, j, k;</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">  for (i = 0; i < C->size; i++) {</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">    for (j = 0; j < C->size; j++) {</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">      A->data[i][j] = 0;</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">@@ -302,7 +303,27 @@ void mat_mult_diag(Matrix *A, Matrix *B, Vector *C, Matrix *D) {</td>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">    }</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">  }</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">}</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="309" 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">

309

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="310" 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">

310

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="311" 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">

311

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="315" 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">

315

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="316" 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">

316

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="317" 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">

317

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="318" 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">

318

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="319" 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">

319

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="320" 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">

320

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="321" 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">

321

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

<pre style="margin: 0;">+<span id="LC321" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="322" 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">

322

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="323" 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">

323

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="c"><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>

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

<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"></span>

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<td class="diff-line-num new old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c"><span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">mat_equal</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">Matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">B</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nrows</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nrows</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ncols</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ncols</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<br>

</li>

<li id="120416c598d701c4240159523284871a18a896d7">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#120416c598d701c4240159523284871a18a896d7"><strong>src/lib/msa/maf.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(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="139" style="width: 35px; color: rgba(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">@@ -139,12 +139,10 @@ MSA *maf_read_cats_subset(FILE *F, FILE *REFSEQF, int tuple_size,</td>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c">      <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alloc_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refseqlen</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">//this may still not be big enough because of gaps in refseq</span></span>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span> </span>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c">      <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alloc_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50000</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="142" 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="LC142" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1000000</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> </span>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="142" 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="LC143" class="line" lang="c">                               <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow_bounded</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span> <span class="mi" style="color: #099;">1000000</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c">  <span class="k" style="font-weight: 600;">else</span> </span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="mi" style="color: #099;">1000000</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="145" 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="LC147" class="line" lang="c">                 <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow_bounded</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span> <span class="mi" style="color: #099;">1000000</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10000000</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">max_tuples</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;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000000</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1000000</span><span class="p">)</span> <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000000</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="596" style="width: 35px; color: rgba(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="594" style="width: 35px; color: rgba(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">@@ -596,15 +594,13 @@ MSA *maf_read_unsorted(FILE *F, FILE *REFSEQF, int tuple_size, char *alphabet,</td>

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="c"></span>

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<td class="diff-line-num new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">store_order</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC596" class="line" lang="c">    <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">msa_len</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">refseqlen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="597" 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="LC599" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC600" class="line" lang="c">                     <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="597" 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">

597

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

<pre style="margin: 0;">+<span id="LC597" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow_bounded</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<td class="diff-line-num new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

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<pre style="margin: 0;"> <span id="LC598" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</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;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<td class="diff-line-num new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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

<pre style="margin: 0;"> <span id="LC599" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1000000</span><span class="p">)</span> <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000000</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

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<td class="diff-line-num new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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

<pre style="margin: 0;"> <span id="LC600" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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

<pre style="margin: 0;"> <span id="LC601" class="line" lang="c">  <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<td class="diff-line-num new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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

<pre style="margin: 0;"> <span id="LC602" class="line" lang="c">    <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="606" 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">

606

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC606" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="mi" style="color: #099;">50000</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="607" 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">

607

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC607" class="line" lang="c">                     <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="603" 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">

603

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

<pre style="margin: 0;">+<span id="LC603" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow_bounded</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missing</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span> <span class="mi" style="color: #099;">50000</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<td class="diff-line-num new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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

<pre style="margin: 0;"> <span id="LC604" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</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;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50000</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<td class="diff-line-num new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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

<pre style="margin: 0;"> <span id="LC605" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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

<pre style="margin: 0;"> <span id="LC606" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="440b536fb9362a7a47baa54729f4b22d199d332d">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#440b536fb9362a7a47baa54729f4b22d199d332d"><strong>src/lib/msa/maf_block.c</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <maf_block.h></span></span>

</pre>

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14

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <hashtable.h></span></span>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>

</pre>

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

16

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

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="n" style="color: #333;">MafBlock</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">mafBlock_new</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c">  <span class="n" style="color: #333;">MafBlock</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">block</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">MafBlock</span><span class="p">));</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" style="width: 35px; color: rgba(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="201" style="width: 35px; color: rgba(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">@@ -201,7 +201,10 @@ void mafBlock_add_iLine(String *line, MafSubBlock *sub) {</td>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c">  </span>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC202" 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="mi" style="color: #099;">6</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 class="n" style="color: #333;">str_free</span><span class="p">((</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">lst_get_ptr</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c">  <span class="n" style="color: #333;">lst_free</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: bad MAF file"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c">  <span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineType</span><span class="p">[</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(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="250" style="width: 35px; color: rgba(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">@@ -247,7 +250,9 @@ void mafBlock_add_qLine(String *line, MafSubBlock *sub) {</td>

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<td class="diff-line-num old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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<td class="diff-line-num new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

250

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

<pre style="margin: 0;"> <span id="LC250" class="line" lang="c">   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

248

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<td class="diff-line-num new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<pre style="margin: 0;"> <span id="LC251" 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="mi" style="color: #099;">2</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 class="n" style="color: #333;">str_free</span><span class="p">((</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">lst_get_ptr</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<td class="diff-line-num new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

252

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

<pre style="margin: 0;"> <span id="LC252" class="line" lang="c">  <span class="n" style="color: #333;">lst_free</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="253" 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">

253

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

<pre style="margin: 0;">+<span id="LC253" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: bad MAF file"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

250

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<td class="diff-line-num new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

254

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

<pre style="margin: 0;"> <span id="LC254" class="line" lang="c">  <span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineType</span><span class="p">[</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'q'</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="255" 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">

255

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

<pre style="margin: 0;">+<span id="LC255" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<td class="diff-line-num new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

252

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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

257

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

<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

258

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

<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="710" style="width: 35px; color: rgba(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="715" style="width: 35px; color: rgba(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">@@ -710,7 +715,8 @@ void mafSubBlock_strip_iLine(MafSubBlock *sub) {</td>

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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<td class="diff-line-num new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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

<pre style="margin: 0;"> <span id="LC715" 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;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<td class="diff-line-num new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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

<pre style="margin: 0;"> <span id="LC716" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineType</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'i'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

</td>

<td class="diff-line-num new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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

<pre style="margin: 0;"> <span id="LC717" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</span><span class="p">)</span> <span class="p">{</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="713" 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">

713

</td>

<td class="diff-line-num new_line old" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC713" 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="n" style="color: #333;">i</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</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="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="718" 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">

718

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

<pre style="margin: 0;">+<span id="LC718" class="line" lang="c">    <span class="n" style="color: #333;">assert</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;">4</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="719" 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">

719

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

<pre style="margin: 0;">+<span id="LC719" 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="n" style="color: #333;">i</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numLine</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4</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="p">{</span></span>

</pre>

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714

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720

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<pre style="margin: 0;"> <span id="LC720" class="line" lang="c">      <span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineType</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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineType</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<pre style="margin: 0;"> <span id="LC721" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lineType</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">)</span></span>

</pre>

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716

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722

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<pre style="margin: 0;"> <span id="LC722" class="line" lang="c">    <span class="n" style="color: #333;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR mafSubBlock_strip_iLine: sub->lineType[%i]=%c</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="d531898f3bec32e2718f0bdc23f7a294fbabc041">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#d531898f3bec32e2718f0bdc23f7a294fbabc041"><strong>src/lib/msa/sufficient_stats.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(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="117" style="width: 35px; color: rgba(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">@@ -117,8 +117,8 @@ void ss_from_msas(MSA *msa, int tuple_size, int store_order,</td>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c">      <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source_msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ntuples</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">source_msa</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source_msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_NTUPLE_ALLOC</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="120" 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">

120

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<td class="diff-line-num new_line old" data-linenumber="120" 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="LC120" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">min</span></span><span class="p"><span class="idiff">((</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">pow</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">alphabet</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">missing</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>

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<td class="diff-line-num old old_line" data-linenumber="121" 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">

121

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<td class="diff-line-num new_line old" data-linenumber="120" 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="LC121" class="line" lang="c">                         <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p"><span class="idiff left right">),</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c">    <span class="n" style="color: #333;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">pow_bounded</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">alphabet</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">missing</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c">                         <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p"><span class="idiff left">,</span></span><span class="idiff right">   </span></span>

</pre>

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122

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<td class="diff-line-num new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c">                     <span class="n" style="color: #333;">upper_bound</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</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;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">upper_bound</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">//protect against overflow</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c">    <span class="n" style="color: #333;">ss_new</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span> <span class="n" style="color: #333;">max_tuples</span><span class="p">,</span> <span class="n" style="color: #333;">do_cats</span><span class="p">,</span> <span class="n" style="color: #333;">store_order</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(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="139" style="width: 35px; color: rgba(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">@@ -139,8 +139,8 @@ void ss_from_msas(MSA *msa, int tuple_size, int store_order,</td>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c">      <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ntuples</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">source_msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ntuples</span><span class="p">;</span></span>

</pre>

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140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c">      <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ntuples</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">source_msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left">max_tuples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">min</span></span><span class="p"><span class="idiff">((</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">pow</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">alphabet</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">missing</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>

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<td class="diff-line-num old old_line" data-linenumber="143" 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">

143

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<td class="diff-line-num new_line old" data-linenumber="142" 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="LC143" class="line" lang="c">                         <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p"><span class="idiff left right">)</span>,</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c">    <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">max_tuples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pow_bounded</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">alphabet</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">strlen</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">missing</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">,</span></span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c">                         <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c">                     <span class="n" style="color: #333;">upper_bound</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_tuples</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;">max_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">upper_bound</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c">    <span class="n" style="color: #333;">ss_realloc</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">tuple_size</span><span class="p">,</span> <span class="n" style="color: #333;">max_tuples</span><span class="p">,</span> <span class="n" style="color: #333;">do_cats</span><span class="p">,</span> <span class="n" style="color: #333;">store_order</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="e000079933b4c58bf725cd26e5d22c166063d58c">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#e000079933b4c58bf725cd26e5d22c166063d58c"><strong>src/make-include.mk</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="133" style="width: 35px; color: rgba(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">@@ -133,7 +133,7 @@ endif</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"># vecLib</span>

</pre>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">ifdef VECLIB</span>

</pre>

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135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext">CFLAGS += -DVECLIB</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="136" 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="LC136" class="line" lang="plaintext">LIBS = -lphast -framework <span class="idiff left right">vecLib</span> -lc -lm</span>

</pre>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">LIBS = -lphast -framework <span class="idiff left right">Accelerate</span> -lc -lm</span>

</pre>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"># CLAPACK</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">else</span>

</pre>

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<br>

</li>

<li id="cbef062acd6c7d49ab15921df473b83bd2b10c07">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#cbef062acd6c7d49ab15921df473b83bd2b10c07"><strong>src/util/clean_genes.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">@@ -34,16 +34,16 @@</td>

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34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span><span class="n" style="color: #333;">OKAY</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_REF</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_REF_START</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_REF_STOP</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_REF_5_SPLICE</span><span class="p">,</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c">              <span class="n" style="color: #333;">BAD_REF_3_SPLICE</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_REF_ORF</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_REF_INDEL_STRICT_FAIL</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c">              <span class="n" style="color: #333;">NO_ALN</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_START</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_STOP</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_5_SPLICE</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_3_SPLICE</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="37" 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="LC37" class="line" lang="c">              <span class="n" style="color: #333;">BAD_5_SPLICE_UTR</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_3_SPLICE_UTR</span><span class="p">,</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">,</span> <span class="n" style="color: #333;">FSHIFT</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="37" 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="LC38" class="line" lang="c">              <span class="n" style="color: #333;">BAD_INTRON</span><span class="p">,</span> <span class="n" style="color: #333;">TOO_MANY_Ns</span><span class="p">,</span> <span class="n" style="color: #333;">WARN_FSHIFT</span><span class="p">,</span> <span class="n" style="color: #333;">WARN_Ns</span><span class="p">,</span> <span class="n" style="color: #333;">NTYPES</span><span class="p">}</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c">              <span class="n" style="color: #333;">BAD_5_SPLICE_UTR</span><span class="p">,</span> <span class="n" style="color: #333;">BAD_3_SPLICE_UTR</span><span class="p">,</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">,</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c">              <span class="n" style="color: #333;">BAD_INTRON</span><span class="p">,</span> <span class="n" style="color: #333;">TOO_MANY_Ns</span><span class="p">,</span> <span class="n" style="color: #333;">WARN_F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">,</span> <span class="n" style="color: #333;">WARN_Ns</span><span class="p">,</span> <span class="n" style="color: #333;">NTYPES</span><span class="p">}</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="n" style="color: #333;">status_type</span><span class="p">;</span>                    <span class="cm" style="color: #998; font-style: italic;">/* NTYPES marks the total number */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC41" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* possible gap types for cds exon -- frame-shift gaps (FSHIFT_BAD),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   no apparent frame shift (FSHIFT_OK), all gaps multiple of 3 in len</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* possible gap types for cds exon -- frame-shift gaps (F<span class="idiff left right">RAME</span>SHIFT_BAD),</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   no apparent frame shift (F<span class="idiff left right">RAME</span>SHIFT_OK), all gaps multiple of 3 in len</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   (CLN_GAPS), gaps mult. of 3 and nonoverlapping (NOVRLP_CLN_GAPS),</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   and no gaps present (NGAPS).  Defined in order of least to most</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   stringent criterion (ordering gets used) */</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span><span class="n" style="color: #333;">F<span class="idiff left">SHIFT_BAD</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">F</span>SHIFT_OK</span><span class="p">,</span> <span class="n" style="color: #333;">CLN_GAPS</span><span class="p">,</span> </span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span><span class="n" style="color: #333;">F<span class="idiff left">RAMESHIFT_BAD</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FRAME</span>SHIFT_OK</span><span class="p">,</span> <span class="n" style="color: #333;">CLN_GAPS</span><span class="p">,</span> </span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c">              <span class="n" style="color: #333;">NOVRLP_CLN_GAPS</span><span class="p">,</span> <span class="n" style="color: #333;">NGAPS</span><span class="p">,</span> <span class="n" style="color: #333;">NGAP_TYPES</span><span class="p">}</span> </span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="n" style="color: #333;">cds_gap_type</span><span class="p">;</span>                   <span class="cm" style="color: #998; font-style: italic;">/* NGAP_TYPES marks the total number */</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"></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">@@ -102,7 +102,7 @@ typedef struct Problem {</td>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c">  <span class="n" style="color: #333;">status_type</span> <span class="n" style="color: #333;">status</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c">  <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">cds_gap</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/* if status if FSHIFT */</span></span>

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<td class="diff-line-num new old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c">  <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">cds_gap</span><span class="p">;</span>  <span class="cm" style="color: #998; font-style: italic;">/* if status if F<span class="idiff left right">RAME</span>SHIFT */</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">Problem</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* create a new problem.  feat can be null for whole gene.</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="311" style="width: 35px; color: rgba(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">@@ -311,7 +311,7 @@ int gap_compare(const void *ptr1, const void* ptr2) {</td>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">g1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* scans a cds for gaps.  Returns CLN_GAPS, NOVRLP_CLN_GAPS, NO_GAPS,</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   or FSHIFT_BAD; doesn't try to check for compensatory indels, which</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   or F<span class="idiff left right">RAME</span>SHIFT_BAD; doesn't try to check for compensatory indels, which</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   is more complicated (this is left for the special-purpose function</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   below) */</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">scan_for_gaps</span><span class="p">(</span><span class="n" style="color: #333;">GFF_Feature</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">Problem</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">problem</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(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="322" style="width: 35px; color: rgba(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">@@ -322,7 +322,7 @@ int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {</td>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c">  <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NGAPS</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c">  <span class="n" style="color: #333;">List</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lst_new_ptr</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC325" 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;">retval</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FSHIFT_BAD</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</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="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC325" 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;">retval</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseqs</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="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC326" 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="n" style="color: #333;">msa_start</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;">msa_end</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 class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ss_get_char_pos</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">i</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="n" style="color: #333;">GAP_CHAR</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gap_start</span><span class="p">,</span> <span class="n" style="color: #333;">gap_end</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="336" style="width: 35px; color: rgba(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="336" style="width: 35px; color: rgba(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">@@ -336,9 +336,9 @@ int scan_for_gaps(GFF_Feature *feat, MSA *msa, Problem **problem) {</td>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="c">        <span class="n" style="color: #333;">gap_end</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span>              <span class="cm" style="color: #998; font-style: italic;">/* inclusive */</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gap_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gap_start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="c">          <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_BAD</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c">          <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">problem_new</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">FSHIFT</span><span class="p">,</span> <span class="n" style="color: #333;">gap_start</span><span class="p">,</span> <span class="n" style="color: #333;">gap_end</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="341" 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="LC341" class="line" lang="c">          <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problem</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_BAD</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c">          <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="c">          <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">problem_new</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">,</span> <span class="n" style="color: #333;">gap_start</span><span class="p">,</span> <span class="n" style="color: #333;">gap_end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="c">          <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problem</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c">          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="449" style="width: 35px; color: rgba(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="449" style="width: 35px; color: rgba(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">@@ -449,18 +449,18 @@ int is_fshift_okay(GFF_Feature *feat, MSA *msa) {</td>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   "clean" gaps (all multiples of 3 in length; CLEAN_GAPS)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   non-overlapping clean gaps (NOVRLP_CLN_GAPS), "okay" gaps (only</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   temporary frame shifts, corrected by compensatory indels;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="452" 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="LC452" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   F<span class="idiff left right">SHIFT_OK), or real frame-shift gaps (F</span>SHIFT_BAD) */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">   F<span class="idiff left right">RAMESHIFT_OK), or real frame-shift gaps (FRAME</span>SHIFT_BAD) */</span></span>

</pre>

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453

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="c"><span class="n" style="color: #333;">cds_gap_type</span> <span class="nf" style="color: #900; font-weight: 600;">get_cds_gap_type</span><span class="p">(</span><span class="n" style="color: #333;">GFF_Feature</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">MSA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">List</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problems</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="c">  <span class="n" style="color: #333;">Problem</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problem</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_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="c">  <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scan_for_gaps</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">problem</span><span class="p">);</span></span>

</pre>

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456

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="457" 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="LC457" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FSHIFT_BAD</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_fshift_okay</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="457" 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="LC458" class="line" lang="c">    <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_OK</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_fshift_okay</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="c">    <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_OK</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="c">                                <span class="cm" style="color: #998; font-style: italic;">/* most of the time the call to</span></span>

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<td class="diff-line-num old_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                                   is_fshift_okay won't be</span></span>

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<td class="diff-line-num old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                                   necessary */</span></span>

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<td class="diff-line-num old old_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="462" 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="LC462" class="line" lang="c">    <span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WARN_FSHIFT</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="462" 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="LC463" class="line" lang="c">    <span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_OK</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="c">    <span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WARN_F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="c">    <span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_OK</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

464

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<td class="diff-line-num new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

464

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

465

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<td class="diff-line-num new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

465

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">problem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

466

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<td class="diff-line-num new_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

466

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c">    <span class="n" style="color: #333;">lst_push_ptr</span><span class="p">(</span><span class="n" style="color: #333;">problems</span><span class="p">,</span> <span class="n" style="color: #333;">problem</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="669" style="width: 35px; color: rgba(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="669" style="width: 35px; color: rgba(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">@@ -669,9 +669,9 @@ void write_log(FILE *logf, GFF_FeatureGroup *group, status_type status,</td>

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669

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<td class="diff-line-num new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

669

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="c">      <span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Nonsense mutation"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="672" 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="LC672" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FSHIFT</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="c">      <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="674" 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">

674

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<td class="diff-line-num new_line old" data-linenumber="674" 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="LC674" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">==</span>  <span class="n" style="color: #333;">FSHIFT_OK</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">==</span>  <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_OK</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

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<td class="diff-line-num new_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="c">          <span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Frame-shift gap [gaps not clean]"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="c">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cds_gap</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">CLN_GAPS</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

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<td class="diff-line-num new_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC677" class="line" lang="c">          <span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Frame-shift gap [gaps clean but overlapping/near boundary]"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="689" style="width: 35px; color: rgba(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="689" style="width: 35px; color: rgba(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">@@ -689,7 +689,7 @@ void write_log(FILE *logf, GFF_FeatureGroup *group, status_type status,</td>

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689

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<td class="diff-line-num new_line" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

689

</td>

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

<pre style="margin: 0;"> <span id="LC689" class="line" lang="c">      <span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Too many Ns"</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

690

</td>

<td class="diff-line-num new_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

690

</td>

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

<pre style="margin: 0;"> <span id="LC690" class="line" lang="c">      <span class="n" style="color: #333;">print_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

691

</td>

<td class="diff-line-num new_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

691

</td>

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

<pre style="margin: 0;"> <span id="LC691" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</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="692" 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">

692

</td>

<td class="diff-line-num new_line old" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC692" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WARN_FSHIFT</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="692" 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">

692

</td>

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

<pre style="margin: 0;">+<span id="LC692" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WARN_F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

</td>

<td class="diff-line-num new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

</td>

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

<pre style="margin: 0;"> <span id="LC693" class="line" lang="c">      <span class="n" style="color: #333;">reason</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Frame shift gap (with compensatory gap)"</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

</td>

<td class="diff-line-num new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

</td>

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

<pre style="margin: 0;"> <span id="LC694" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

695

</td>

<td class="diff-line-num new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

695

</td>

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

<pre style="margin: 0;"> <span id="LC695" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WARN_Ns</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="741" style="width: 35px; color: rgba(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="741" style="width: 35px; color: rgba(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">@@ -741,13 +741,13 @@ char *status_type_str(status_type status) {</td>

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

<td class="diff-line-num old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="diff-line-num new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

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

<pre style="margin: 0;"> <span id="LC741" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"bad_3_splice_utr"</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

</td>

<td class="diff-line-num new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

</td>

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

<pre style="margin: 0;"> <span id="LC742" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="diff-line-num new_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

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

<pre style="margin: 0;"> <span id="LC743" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"nonsense"</span><span class="p">;</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="744" 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">

744

</td>

<td class="diff-line-num new_line old" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC744" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FSHIFT</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="744" 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">

744

</td>

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

<pre style="margin: 0;">+<span id="LC744" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

<td class="diff-line-num new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

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

<pre style="margin: 0;"> <span id="LC745" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"frameshift"</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

</td>

<td class="diff-line-num new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

</td>

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

<pre style="margin: 0;"> <span id="LC746" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BAD_INTRON</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

</td>

<td class="diff-line-num new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

</td>

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

<pre style="margin: 0;"> <span id="LC747" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"bad_intron"</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

<td class="diff-line-num new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

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

<pre style="margin: 0;"> <span id="LC748" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">TOO_MANY_Ns</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="diff-line-num new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

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

<pre style="margin: 0;"> <span id="LC749" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"too_many_Ns"</span><span class="p">;</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="750" 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">

750

</td>

<td class="diff-line-num new_line old" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC750" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WARN_FSHIFT</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="750" 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">

750

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<pre style="margin: 0;">+<span id="LC750" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WARN_F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

</td>

<td class="diff-line-num new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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<pre style="margin: 0;"> <span id="LC751" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"warning_fshift"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

</td>

<td class="diff-line-num new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

</td>

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

<pre style="margin: 0;"> <span id="LC752" class="line" lang="c">  <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WARN_Ns</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

</td>

<td class="diff-line-num new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

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

<pre style="margin: 0;"> <span id="LC753" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"warning_Ns"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="980" style="width: 35px; color: rgba(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="980" style="width: 35px; color: rgba(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">@@ -980,7 +980,7 @@ int main(int argc, char *argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

980

</td>

<td class="diff-line-num new_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

980

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<pre style="margin: 0;"> <span id="LC980" class="line" lang="c">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">discards</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">intron_splice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lst_new_ptr</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

<td class="diff-line-num new_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

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

<pre style="margin: 0;"> <span id="LC981" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rseq_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

<td class="diff-line-num new_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

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

<pre style="margin: 0;"> <span id="LC982" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">logf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mlogf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">statsf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">discardf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="983" 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">

983

</td>

<td class="diff-line-num new_line old" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC983" class="line" lang="c">  <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_BAD</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="983" 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">

983

</td>

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

<pre style="margin: 0;">+<span id="LC983" class="line" lang="c">  <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

984

</td>

<td class="diff-line-num new_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

984

</td>

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

<pre style="margin: 0;"> <span id="LC984" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">groupby</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"transcript_id"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

</td>

<td class="diff-line-num new_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

</td>

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

<pre style="margin: 0;"> <span id="LC985" class="line" lang="c">  <span class="n" style="color: #333;">msa_coord_map</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">map</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

<td class="diff-line-num new_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

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

<pre style="margin: 0;"> <span id="LC986" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">countNs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">countCDSs</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1029" style="width: 35px; color: rgba(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="1029" style="width: 35px; color: rgba(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">@@ -1029,11 +1029,11 @@ int main(int argc, char *argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1029

</td>

<td class="diff-line-num new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1029

</td>

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

<pre style="margin: 0;"> <span id="LC1029" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

</td>

<td class="diff-line-num new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

</td>

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

<pre style="margin: 0;"> <span id="LC1030" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

</td>

<td class="diff-line-num new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

</td>

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

<pre style="margin: 0;"> <span id="LC1031" class="line" lang="c">      <span class="n" style="color: #333;">check_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1032" 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">

1032

</td>

<td class="diff-line-num new_line old" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1032" class="line" lang="c">      <span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_OK</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1032" 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">

1032

</td>

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

<pre style="margin: 0;">+<span id="LC1032" class="line" lang="c">      <span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_OK</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

</td>

<td class="diff-line-num new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

</td>

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

<pre style="margin: 0;"> <span id="LC1033" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

<td class="diff-line-num new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

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

<pre style="margin: 0;"> <span id="LC1034" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1035

</td>

<td class="diff-line-num new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1035

</td>

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

<pre style="margin: 0;"> <span id="LC1035" class="line" lang="c">      <span class="n" style="color: #333;">check_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_splice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_nonsense</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</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="1036" 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">

1036

</td>

<td class="diff-line-num new_line old" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1036" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">F<span class="idiff left">SHIFT_OK</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fshift_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">F</span>SHIFT_OK</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1036" 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">

1036

</td>

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

<pre style="margin: 0;">+<span id="LC1036" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">F<span class="idiff left">RAMESHIFT_OK</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fshift_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FRAME</span>SHIFT_OK</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1037

</td>

<td class="diff-line-num new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1037

</td>

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

<pre style="margin: 0;"> <span id="LC1037" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1038

</td>

<td class="diff-line-num new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1038

</td>

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

<pre style="margin: 0;"> <span id="LC1038" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1039

</td>

<td class="diff-line-num new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1039

</td>

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

<pre style="margin: 0;"> <span id="LC1039" class="line" lang="c">      <span class="n" style="color: #333;">Nfrac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_arg_dbl_bounds</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1166" style="width: 35px; color: rgba(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="1166" style="width: 35px; color: rgba(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">@@ -1166,7 +1166,7 @@ int main(int argc, char *argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

</td>

<td class="diff-line-num new_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

</td>

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

<pre style="margin: 0;"> <span id="LC1166" class="line" lang="c">    <span class="n" style="color: #333;">List</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gfeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">features</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

</td>

<td class="diff-line-num new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

</td>

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

<pre style="margin: 0;"> <span id="LC1167" class="line" lang="c">    <span class="n" style="color: #333;">GFF_Feature</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">feat</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1168

</td>

<td class="diff-line-num new_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1168

</td>

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

<pre style="margin: 0;"> <span id="LC1168" class="line" lang="c">    <span class="n" style="color: #333;">status_type</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OKAY</span><span class="p">;</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="1169" 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">

1169

</td>

<td class="diff-line-num new_line old" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1169" class="line" lang="c">    <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT_BAD</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1169" 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">

1169

</td>

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

<pre style="margin: 0;">+<span id="LC1169" class="line" lang="c">    <span class="n" style="color: #333;">cds_gap_type</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1170

</td>

<td class="diff-line-num new_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1170

</td>

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

<pre style="margin: 0;"> <span id="LC1170" class="line" lang="c">    <span class="n" style="color: #333;">problems_clear</span><span class="p">(</span><span class="n" style="color: #333;">problems</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1171

</td>

<td class="diff-line-num new_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1171

</td>

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

<pre style="margin: 0;"> <span id="LC1171" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1172

</td>

<td class="diff-line-num new_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1172

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

<pre style="margin: 0;"> <span id="LC1172" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/* make sure have frame info for CDSs */</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1295" style="width: 35px; color: rgba(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="1295" style="width: 35px; color: rgba(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">@@ -1295,9 +1295,9 @@ int main(int argc, char *argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1295

</td>

<td class="diff-line-num new_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1295

</td>

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

<pre style="margin: 0;"> <span id="LC1295" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1296

</td>

<td class="diff-line-num new_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1296

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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="c">          <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">str_equals_charstr</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">GFF_CDS_TYPE</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1297

</td>

<td class="diff-line-num new_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1297

</td>

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

<pre style="margin: 0;"> <span id="LC1297" class="line" lang="c"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1298" 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">

1298

</td>

<td class="diff-line-num new_line old" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1298" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FSHIFT_BAD</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1298" 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">

1298

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

<pre style="margin: 0;">+<span id="LC1298" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fshift_mode</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_BAD</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1299

</td>

<td class="diff-line-num new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1299

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

<pre style="margin: 0;"> <span id="LC1299" class="line" lang="c">           <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_cds_gap_type</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">problems</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">fshift_mode</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1300" 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">

1300

</td>

<td class="diff-line-num new_line old" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1300" class="line" lang="c">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">OKAY</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">)</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FSHIFT</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1300" 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">

1300

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

<pre style="margin: 0;">+<span id="LC1300" class="line" lang="c">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">OKAY</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">)</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1301

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<td class="diff-line-num new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1301

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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1302

</td>

<td class="diff-line-num new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1302

</td>

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

<pre style="margin: 0;"> <span id="LC1302" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1303

</td>

<td class="diff-line-num new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1303

</td>

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

<pre style="margin: 0;"> <span id="LC1303" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_nonsense</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">is_nonsense_clean</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">problems</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1336" style="width: 35px; color: rgba(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="1336" style="width: 35px; color: rgba(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">@@ -1336,8 +1336,8 @@ int main(int argc, char *argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1336

</td>

<td class="diff-line-num new_line" data-linenumber="1336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1336

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

<pre style="margin: 0;"> <span id="LC1336" 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;">lst_size</span><span class="p">(</span><span class="n" style="color: #333;">problems</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="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1337

</td>

<td class="diff-line-num new_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1337

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

<pre style="margin: 0;"> <span id="LC1337" class="line" lang="c">              <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Problem</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">problem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lst_get_ptr</span><span class="p">(</span><span class="n" style="color: #333;">problems</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="c">              <span class="n" style="color: #333;">status_type</span> <span class="n" style="color: #333;">ftype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">status</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1339" 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="LC1339" class="line" lang="c">              <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ftype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FSHIFT</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ftype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1339" 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="LC1340" class="line" lang="c">                  <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FSHIFT</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="c">              <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ftype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ftype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="c">                  <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NONSENSE</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="c">                <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>       <span class="cm" style="color: #998; font-style: italic;">/* don't count secondary frame shifts</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                                   and nonsense mutations */</span> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1350,7 +1350,7 @@ int main(int argc, char *argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="c">          <span class="cm" style="color: #998; font-style: italic;">/* also keep track of the total number of "conserved exons", and</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">             the number having each kind of gap */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1353" 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="LC1353" class="line" lang="c">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">OKAY</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">F<span class="idiff left">SHIFT</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">F</span>SHIFT_OK</span><span class="p">)))</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="c">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">OKAY</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">F<span class="idiff left">RAMESHIFT</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FRAME</span>SHIFT_OK</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="c">            <span class="n" style="color: #333;">nconserved_exons</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1355

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<td class="diff-line-num new_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="c">            <span class="n" style="color: #333;">nce_gap_type</span><span class="p">[</span><span class="n" style="color: #333;">gt</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span>     <span class="cm" style="color: #998; font-style: italic;">/* number of conserved exons having</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1356

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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">                                       given type of gaps */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1429" style="width: 35px; color: rgba(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="1429" style="width: 35px; color: rgba(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">@@ -1429,10 +1429,10 @@ int main(int argc, char *argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1429

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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="c">            <span class="n" style="color: #333;">nconsid</span><span class="p">[</span><span class="n" style="color: #333;">BAD_5_SPLICE</span><span class="p">],</span> <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">BAD_3_SPLICE</span><span class="p">],</span> <span class="n" style="color: #333;">nconsid</span><span class="p">[</span><span class="n" style="color: #333;">BAD_3_SPLICE</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1430

</td>

<td class="diff-line-num new_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="c">            <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">BAD_5_SPLICE_UTR</span><span class="p">],</span> <span class="n" style="color: #333;">nconsid</span><span class="p">[</span><span class="n" style="color: #333;">BAD_5_SPLICE_UTR</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1431

</td>

<td class="diff-line-num new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1431

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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="c">            <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">BAD_3_SPLICE_UTR</span><span class="p">],</span> <span class="n" style="color: #333;">nconsid</span><span class="p">[</span><span class="n" style="color: #333;">BAD_3_SPLICE_UTR</span><span class="p">],</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1432" 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">

1432

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<td class="diff-line-num new_line old" data-linenumber="1432" 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="LC1432" class="line" lang="c">            <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">BAD_INTRON</span><span class="p">],</span> <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">NONSENSE</span><span class="p">],</span> <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">FSHIFT</span><span class="p">],</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="c">            <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">BAD_INTRON</span><span class="p">],</span> <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">NONSENSE</span><span class="p">],</span> <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT</span><span class="p">],</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="c">            <span class="n" style="color: #333;">nfail</span><span class="p">[</span><span class="n" style="color: #333;">TOO_MANY_Ns</span><span class="p">],</span> <span class="n" style="color: #333;">nconserved_exons</span><span class="p">,</span> <span class="n" style="color: #333;">nce_gap_type</span><span class="p">[</span><span class="n" style="color: #333;">NGAPS</span><span class="p">],</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1434

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<td class="diff-line-num new_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1434

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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="c">            <span class="n" style="color: #333;">nce_gap_type</span><span class="p">[</span><span class="n" style="color: #333;">NOVRLP_CLN_GAPS</span><span class="p">],</span> <span class="n" style="color: #333;">nce_gap_type</span><span class="p">[</span><span class="n" style="color: #333;">CLN_GAPS</span><span class="p">],</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1435" 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">

1435

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<td class="diff-line-num new_line old" data-linenumber="1435" 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="LC1435" class="line" lang="c">            <span class="n" style="color: #333;">nce_gap_type</span><span class="p">[</span><span class="n" style="color: #333;">FSHIFT_OK</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1435" 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">

1435

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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="c">            <span class="n" style="color: #333;">nce_gap_type</span><span class="p">[</span><span class="n" style="color: #333;">F<span class="idiff left right">RAME</span>SHIFT_OK</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1436

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<td class="diff-line-num new_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1436

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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">statsf</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">STATS_DESCRIPTION</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1438

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<td class="diff-line-num new_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="53f2934d07552d00f50907ed7dce7be0e031c466">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#53f2934d07552d00f50907ed7dce7be0e031c466"><strong>src/util/msa_view.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="627" style="width: 35px; color: rgba(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="627" style="width: 35px; color: rgba(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">@@ -627,7 +627,7 @@ int main(int argc, char* argv[]) {</td>

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<td class="diff-line-num old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<td class="diff-line-num new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">GFF_NULL_FRAME</span><span class="p">)</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fourD_refseq</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">fourD_refseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_new_charstr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqname</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chars</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

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<td class="diff-line-num new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c">      <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">str_equals</span><span class="p">(</span><span class="n" style="color: #333;">fourD_refseq</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqname</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="630" 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">

630

</td>

<td class="diff-line-num new_line old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC630" class="line" lang="c">    <span class="n" style="color: #333;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"--4d requires all features <span class="idiff left right">have same source column</span>"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" 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">

630

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

<pre style="margin: 0;">+<span id="LC630" class="line" lang="c">    <span class="n" style="color: #333;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"--4d requires all features <span class="idiff left right">are on the same chromosome</span>"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">str_equals_charstr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<td class="diff-line-num new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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

<pre style="margin: 0;"> <span id="LC632" class="line" lang="c">    <span class="n" style="color: #333;">str_cpy_charstr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDSplus"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

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<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c">      <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">str_equals_charstr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span></span>

</pre>

</td>

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<br>

</li>

<li id="0c4b050bc0a22bd9db927801a888e21a58e2721d">

<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#0c4b050bc0a22bd9db927801a888e21a58e2721d"><strong>test/test_phast.sh</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,39 +37,39 @@ tree_doctor --scale 3.0 hpmr.mod > hpmr_fast.mod</td>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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

<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">********************</span> phyloP <span class="k" style="font-weight: 600;">********************</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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

<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell">phyloFit hmrc.ss <span class="nt" style="color: navy;">--tree</span> <span class="s2" style="color: #d14;">"(human, (mouse,rat), cow)"</span> <span class="nt" style="color: navy;">--quiet</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line old" data-linenumber="40" 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="LC40" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--null</span> 10 phyloFit.mod</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" 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">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--null</span> 10 phyloFit.mod</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell">msa_view <span class="nt" style="color: navy;">-o</span> SS <span class="nt" style="color: navy;">--end</span> 100 hmrc.ss <span class="o" style="font-weight: 600;">></span> hmrc_short.ss</span>

</pre>

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

42

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell">@phyloP phyloFit.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" 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">

43

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</span>

</pre>

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

44

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</span>

</pre>

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45

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">-d</span> 12345 <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--mode</span> NNEUT <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</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="46" 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">

46

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> GERP <span class="nt" style="color: navy;">--mode</span> ACC <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</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="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

</td>

<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> GERP <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</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="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

</td>

<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">-d</span> 12345 <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</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="49" 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">

49

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</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="50" 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">

50

</td>

<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</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="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">-d</span> 12345 <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--wig-scores</span> <span class="nt" style="color: navy;">--refidx</span> 2 phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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

<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span>phyloFit.mod hmrc_short.ss</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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

<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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

<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

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

45

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

<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">-d</span> 12345 <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--mode</span> NNEUT <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

</td>

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

<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> GERP <span class="nt" style="color: navy;">--mode</span> ACC <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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

<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> GERP <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

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

48

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

<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">-d</span> 12345 <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

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

<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--wig-scores</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

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

50

</td>

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

<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--base-by-base</span> phyloFit.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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

<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">-d</span> 12345 <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--wig-scores</span> <span class="nt" style="color: navy;">--refidx</span> 2 phyloFit.mod hmrc.ss</span>

</pre>

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52

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-e</span> <span class="s2" style="color: #d14;">"chr1</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">10</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">chr1</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">50</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">100</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">chr1</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">200</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">300"</span> <span class="o" style="font-weight: 600;">></span> temp.bed</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

53

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" 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">

54

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--features</span> temp.bed <span class="nt" style="color: navy;">-g</span> phyloFit.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--features</span> temp.bed <span class="nt" style="color: navy;">-g</span> phyloFit.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

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

<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell">tree_doctor <span class="nt" style="color: navy;">--name-ancestors</span> phyloFit.mod <span class="o" style="font-weight: 600;">></span> phyloFit-named.mod</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" 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">

56

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> ACC <span class="nt" style="color: navy;">--branch</span> mouse-rat <span class="nt" style="color: navy;">-w</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--posterior</span> phyloFit.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--fit-model</span> <span class="nt" style="color: navy;">-w</span> <span class="nt" style="color: navy;">--subtree</span> mouse-rat phyloFit-named.mod hmrc_short.ss</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--epsilon</span> 0.0001 phyloFit-named.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--confidence-interval</span> 0.05 phyloFit-named.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--quantiles</span> <span class="nt" style="color: navy;">--null</span> 100 phyloFit-named.mod</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--mode</span> ACC <span class="nt" style="color: navy;">--branch</span> mouse-rat <span class="nt" style="color: navy;">-w</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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

<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--posterior</span> phyloFit.mod hmrc_short.ss</span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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

<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--fit-model</span> <span class="nt" style="color: navy;">-w</span> <span class="nt" style="color: navy;">--subtree</span> mouse-rat phyloFit-named.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--epsilon</span> 0.0001 phyloFit-named.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--confidence-interval</span> 0.05 phyloFit-named.mod hmrc_short.ss</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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

<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--quantiles</span> <span class="nt" style="color: navy;">--null</span> 100 phyloFit-named.mod</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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

<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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

<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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

<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># want to try subtree with LRT, SCORE, SPH, with both --base-by-base and --features</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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

<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># note that bugs in SCORE method mean tests will fail against revisions < 6563</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="67" 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">

67

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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

68

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC68" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC70" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="71" 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">

71

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> SPH <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell">@phyloP <span class="nt" style="color: navy;">--method</span> SPH <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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

<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> LRT <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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

<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> SCORE <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit-named.mod hmrc.ss</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="71" 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">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> SPH <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--base-by-base</span> phyloFit-named.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="72" 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">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell">@phyloP <span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">--seed</span></span><span class="idiff right"> 123 </span><span class="nt" style="color: navy;">--method</span> SPH <span class="nt" style="color: navy;">--subtree</span> mouse-rat <span class="nt" style="color: navy;">--mode</span> CONACC <span class="nt" style="color: navy;">--features</span> temp.bed phyloFit-named.mod hmrc.ss</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> hmrc_short.ss phyloFit.mod phyloFit-named.mod temp.bed</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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

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

</pre>

</td>

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<a href="https://salsa.debian.org/med-team/phast/commit/01c9ee8d01efbf8b89e9b016104a7f0ba07d0741#c692273deb2772da307ffe37041fef77bf4baa97"><strong>version</strong></a>

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

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1

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

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">v1.<span class="idiff left right">3</span></span></pre>

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

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1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">v1.<span class="idiff left right">4</span></span></pre>

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