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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/8e430e2ca0158e260b1ca99993f2d5fb0f1cc72d">8e430e2c</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-04-14T15:27:03+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.14</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
align.c
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<li class="file-stats">
<a href="#596ab94993f840fb54df19a92f10da821eccfa7a">
chain.c
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<li class="file-stats">
<a href="#f966218212bf61b9bacc17a9bc23ef9ad756be7c">
chain.h
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<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
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<li class="file-stats">
<a href="#97e3379ce2e33418ea5b83d3faaf35326b973d41">
nw.c
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<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
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<h4>Changes:</h4>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/-/commit/8e430e2ca0158e260b1ca99993f2d5fb0f1cc72d#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.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">@@ -226,6 +226,9 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Stat</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim seeds */</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">trimSeeds</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize */</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">Stat</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<li id="596ab94993f840fb54df19a92f10da821eccfa7a">
<a href="https://salsa.debian.org/med-team/kma/-/commit/8e430e2ca0158e260b1ca99993f2d5fb0f1cc72d#596ab94993f840fb54df19a92f10da821eccfa7a"><strong>chain.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(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="137" style="width: 35px; color: rgba(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">@@ -137,12 +137,13 @@ int chainSeeds(AlnPoints *points, int q_len, int t_len, int kmersize, unsigned *</td>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</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="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check if score is max */</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;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="p">}</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">@@ -194,14 +195,12 @@ int chainSeeds(AlnPoints *points, int q_len, int t_len, int kmersize, unsigned *</td>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</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="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update bestScore */</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">bestPos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="p">}</span> <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;">bestScore</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">bestPos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate mapping quality */</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">@@ -284,12 +283,13 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</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="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check if score is max */</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"> <span class="p">}</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">@@ -327,6 +327,7 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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;">2</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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;">Ms</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</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="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span><span class="p">;</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">@@ -353,7 +354,7 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="c"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</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="p">(</span><span class="n" style="color: #333;">tStart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tEnd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check if score is max */</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">gap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(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="391" style="width: 35px; color: rgba(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">@@ -390,14 +391,12 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</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="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update bestScore */</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">bestPos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> <span class="n" style="color: #333;">bestPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"> <span class="p">}</span> <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;">bestScore</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</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="n" style="color: #333;">bestPos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">secondScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* calculate mapping quality */</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">@@ -417,3 +416,31 @@ int chainSeeds_circular(AlnPoints *points, int q_len, int t_len, int kmersize, u</td>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestPos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trimSeeds</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim the start of each seed */</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">points</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="c"> <span class="n" style="color: #333;">ts</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="LC428" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="c"> <span class="p">}</span> <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;">ts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* iterate seeds on best chain */</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="c"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim seed */</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qEnd</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* ensure at least one nucleotide remains in seed */</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qStart</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]));</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="c"><span class="p">}</span></span></pre>
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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">@@ -45,3 +45,4 @@ void seedPoint_realloc(AlnPoints *dest, int size);</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">seedPoint_free</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chainSeeds</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mapQ</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chainSeeds_circular</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mapQ</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trimSeeds</span><span class="p">(</span><span class="n" style="color: #333;">AlnPoints</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">points</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span></pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -113,6 +113,7 @@ static void helpMessage(int exeStatus) {</td>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-ipe</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Input paired end file name(s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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114
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-int</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Input interleaved file name(s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-k</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Kmersize</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"DB defined"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-ts</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Trim front of seeds with ts</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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116
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-ml</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum alignment length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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117
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-p</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">p-value</span><span class="se" style="color: #d14;">\t\t\t\t</span><span class="s" style="color: #d14;">0.05</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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118
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-ConClave</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ConClave version</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</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">@@ -203,7 +204,7 @@ int kma_main(int argc, char *argv[]) {</td>
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203
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">Ts</span><span class="p">,</span> <span class="n" style="color: #333;">Tv</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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204
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">spltDB</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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205
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">one2one</span><span class="p">;</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sparse_run</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sparse_run</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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207
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>
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208
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">;</span></span>
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -251,6 +252,7 @@ int kma_main(int argc, char *argv[]) {</td>
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251
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">print_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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252
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">ref_fsa</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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253
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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254
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">minlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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255
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">;</span></span>
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256
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">support</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="504" style="width: 35px; color: rgba(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="506" style="width: 35px; color: rgba(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">@@ -504,6 +506,15 @@ int kma_main(int argc, char *argv[]) {</td>
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504
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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505
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="c"> <span class="p">}</span></span>
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506
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"> <span class="p">}</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"> <span class="p">}</span> <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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-ts"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoul</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exeBasic</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">30</span><span class="p">)</span> <span class="p">{</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Invalid seed trim parsed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="p">}</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="p">}</span></span>
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507
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="c"> <span class="p">}</span> <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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-ml"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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508
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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509
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<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">@@ -969,6 +980,7 @@ int kma_main(int argc, char *argv[]) {</td>
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969
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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;">args</span><span class="p">;</span></span>
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970
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="c"> <span class="p">}</span></span>
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971
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982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="c"> <span class="n" style="color: #333;">preseed</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="n" style="color: #333;">exhaustive</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="c"> <span class="n" style="color: #333;">trimSeeds</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">);</span></span>
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972
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984
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<pre style="margin: 0;"> <span id="LC984" class="line" lang="c"> </span>
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973
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985
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<pre style="margin: 0;"> <span id="LC985" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">kmaPipe</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmaPipeThread</span><span class="p">)</span> <span class="p">{</span></span>
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974
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986
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<pre style="margin: 0;"> <span id="LC986" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-sam</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> and </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-status</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> cannot coincide.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<li id="97e3379ce2e33418ea5b83d3faaf35326b973d41">
<a href="https://salsa.debian.org/med-team/kma/-/commit/8e430e2ca0158e260b1ca99993f2d5fb0f1cc72d#97e3379ce2e33418ea5b83d3faaf35326b973d41"><strong>nw.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" style="width: 35px; color: rgba(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">@@ -183,8 +183,8 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Q_prev</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</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 right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">Q</span></span><span class="p">;</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">D_ptr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">n</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="n" style="color: #333;"><span class="idiff right">thisScore</span></span><span class="p">)</span> <span class="p">{</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">thisScore</span></span><span class="p">;</span></span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="p">}</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(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="193" style="width: 35px; color: rgba(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">@@ -193,7 +193,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,</td>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_prev</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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197
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="483" style="width: 35px; color: rgba(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">@@ -483,8 +483,8 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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483
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Q_prev</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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484
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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485
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485
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c"> <span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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486
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</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 right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">Q</span></span><span class="p">;</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">D_ptr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">n</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="n" style="color: #333;"><span class="idiff right">thisScore</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">thisScore</span></span><span class="p">;</span></span>
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488
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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489
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="p">}</span></span>
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490
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="493" style="width: 35px; color: rgba(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">@@ -493,7 +493,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i</td>
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493
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_prev</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">U</span><span class="p">;</span></span>
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494
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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495
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="c"> <span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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497
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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498
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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499
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="784" style="width: 35px; color: rgba(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="784" style="width: 35px; color: rgba(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">@@ -784,8 +784,8 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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784
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Q_prev</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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785
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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786
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="c"> <span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</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 right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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788
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">Q</span></span><span class="p">;</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">D_ptr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">n</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="n" style="color: #333;"><span class="idiff right">thisScore</span></span><span class="p">)</span> <span class="p">{</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">thisScore</span></span><span class="p">;</span></span>
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789
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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790
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="c"> <span class="p">}</span></span>
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791
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="794" style="width: 35px; color: rgba(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="794" style="width: 35px; color: rgba(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">@@ -794,7 +794,7 @@ AlnScore NW_score(const long unsigned *template, const unsigned char *queryOrg,</td>
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794
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_prev</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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795
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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796
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="c"> <span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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797
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<td class="new_line diff-line-num old" data-linenumber="797" 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="LC797" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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798
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
799
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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800
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1049" style="width: 35px; color: rgba(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="1049" style="width: 35px; color: rgba(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">@@ -1049,8 +1049,8 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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1049
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1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Q_prev</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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1050
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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1051
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<td class="new_line diff-line-num" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="c"> <span class="n" style="color: #333;">Q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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1052
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<td class="new_line diff-line-num old" data-linenumber="1052" 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="LC1052" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</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 right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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1053
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<td class="new_line diff-line-num old" data-linenumber="1052" 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="LC1053" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">Q</span></span><span class="p">;</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">D_ptr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">n</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="n" style="color: #333;"><span class="idiff right">thisScore</span></span><span class="p">)</span> <span class="p">{</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">thisScore</span></span><span class="p">;</span></span>
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1054
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1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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1055
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="c"> <span class="p">}</span></span>
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1056
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1059" style="width: 35px; color: rgba(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="1059" style="width: 35px; color: rgba(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">@@ -1059,7 +1059,7 @@ AlnScore NW_band_score(const long unsigned *template, const unsigned char *query</td>
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1059
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1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="c"> <span class="n" style="color: #333;">thisScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">P_prev</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">U</span><span class="p">;</span></span>
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1060
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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1061
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="c"> <span class="n" style="color: #333;">P_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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1062
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<pre style="margin: 0;">-<span id="LC1062" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">thisScore</span><span class="p">)</span> <span class="p">{</span></span>
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1063
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="c"> <span class="n" style="color: #333;">D_ptr</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisScore</span><span class="p">;</span></span>
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1064
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/8e430e2ca0158e260b1ca99993f2d5fb0f1cc72d#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.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">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" 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="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.1<span class="idiff left right">3</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.3.1<span class="idiff left right">4</span>"</span></span></pre>
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