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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd">cf76fa7e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-28T22:21:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1243</pre>
</li>
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<h4>20 changed files:</h4>
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<li class="file-stats">
<a href="#2eec104bd40706dceb555b7fffb342760f3cbc59">
bin/last-train
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<li class="file-stats">
<a href="#6da0343fd1e96c9faaa35ff4e058c0bb04191144">
doc/last-cookbook.rst
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<li class="file-stats">
<a href="#e6aa9861192a0b058083f4ef525daf93befa49e4">
doc/last-split.rst
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<li class="file-stats">
<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">
src/Alignment.cc
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<li class="file-stats">
<a href="#76a46dca9f85ee73b2a8d67a89f4b9bf80c34b4b">
src/Centroid.cc
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<li class="file-stats">
<a href="#7cc18ac8f8022614b0ff31ec1eeb4152cd88880e">
src/Centroid.hh
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<li class="file-stats">
<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">
src/LastalArguments.cc
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<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
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<li class="file-stats">
<a href="#2bf93e35d0ba974fe4be041c601814d14b253461">
src/split/cbrc_unsplit_alignment.cc
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<li class="file-stats">
<a href="#fc998af53d94055438c79cc84b23acd0ff926b3f">
src/split/cbrc_unsplit_alignment.hh
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<li class="file-stats">
<a href="#a966121261c9a9a0627d40ae5e6f8274fe2ecc88">
src/split/last-split-main.cc
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<li class="file-stats">
<a href="#cff6a16c49a626871ebb6399a31650f25e4f5395">
src/split/last-split.cc
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<li class="file-stats">
<a href="#1ff8d7bf4c81a5aff15c760fc2da99164983b701">
src/split/last-split.hh
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<li class="file-stats">
<a href="#7294d22a62972c98e3d0cae607335ab651731ea8">
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+
test/alli.fa
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<li class="file-stats">
<a href="#b9b7e0ba489bbe86e4faf91536af5aadf40107c5">
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+
test/huma.fa
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<li class="file-stats">
<a href="#67a6c42c3d9e350d422617435e9cb54c619cd2e6">
test/last-split-test.out
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<li class="file-stats">
<a href="#ee216b9a6e5260afd4420396b9136119dc88bb38">
test/last-split-test.sh
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<li class="file-stats">
<a href="#6c90adec85ff9834658c43a287e5d780f52732ef">
test/last-test.out
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<li class="file-stats">
<a href="#fcd3167fe23623673ee838f0da31855d3d479dff">
test/last-test.sh
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<li class="file-stats">
<a href="#3aad58d94722f885e09fe11af2ffb43e844e3ba2">
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+
test/split1.maf
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<h4>Changes:</h4>
<li id="2eec104bd40706dceb555b7fffb342760f3cbc59">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#2eec104bd40706dceb555b7fffb342760f3cbc59"><strong>bin/last-train</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="299" style="width: 35px; color: rgba(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">@@ -299,7 +299,7 @@ def balancedEndProb(*args):</td>
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<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rootOfIncreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">probImbalance</span><span class="p">,</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="302" 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="LC302" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxGapGrowProb</span></span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">matches</span><span class="p">,</span> <span class="n" style="color: #333;">deletes</span><span class="p">,</span> <span class="n" style="color: #333;">inserts</span><span class="p">,</span> <span class="n" style="color: #333;">delOpens</span><span class="p">,</span> <span class="n" style="color: #333;">insOpens</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts</span></span>
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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deletes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">inserts</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delOpens</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insOpens</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -329,6 +329,8 @@ def gapProbsFromCounts(counts, opts):</td>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# delExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# insExtendProb: %g"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">delGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">delGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">maxGapGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">insGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">insGrowProb</span><span class="p">,</span> <span class="n" style="color: #333;">maxGapGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">delOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">delGrowProb</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">insOpenProb</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowProb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapRatiosFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">matchProb</span><span class="p">,</span> <span class="n" style="color: #333;">delProbs</span><span class="p">,</span> <span class="n" style="color: #333;">insProbs</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">@@ -366,13 +368,12 @@ def matScoresFromProbs(scale, matchRatio, matProbs, rowProbs, colProbs):</td>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[[</span><span class="n" style="color: #333;">scoreFromLetterProbs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">colProbs</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">rowProbs</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">isBigScale</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">firstGapRatio</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendRatio</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">firstGapRatio</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendRatio</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The next addition gets the alignment parameter from the path</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parameters, as in Supplementary section 3.1 of [Fri19]:</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">gapExtendRatio</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">firstGapRatio</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This isBigScale aims to avoid ALP failures, and improve speed</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">firstGapCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">firstGapRatio</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">isBigScale</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">gapExtendCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendRatio</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">isBigScale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">firstGapCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">firstGapRatio</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">gapExtendCost</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">costFromProb</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendRatio</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">firstGapCost</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendCost</span></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">imbalanceFromGap</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">firstGapCost</span><span class="p">,</span> <span class="n" style="color: #333;">gapExtendCost</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">@@ -412,11 +413,11 @@ def balancedScale(imbalanceFunc, nearScale, args):</td>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">oldUpper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newUpper</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">scoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isInner</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">scoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScoresFromProbs</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matParams</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">isInner</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;">delRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">insCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">isInner</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;">insRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">delCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">delRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">insCosts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCostsFromProbRatios</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">balancedScale</span><span class="p">(</span><span class="n" style="color: #333;">scoreImbalance</span><span class="p">,</span> <span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -623,7 +624,7 @@ def normalizedFreqs(freqs):</td>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">codonScoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">junk</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">codonScoresAndScale</span><span class="p">(</span><span class="n" style="color: #333;">originalScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowFreqs</span><span class="p">,</span> <span class="n" style="color: #333;">colFreqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matParams</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalizedFreqs</span><span class="p">(</span><span class="n" style="color: #333;">rowFreqs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalizedFreqs</span><span class="p">(</span><span class="n" style="color: #333;">colFreqs</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">@@ -680,7 +681,7 @@ def writeGapCosts(opts, delCosts, insCosts, isLastFormat, outFile):</td>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# frameshiftCosts del-1,del-2,ins+1,ins+2:"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;">codonMatches</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">maxGapGrowProb</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">codonMatches</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lastalArgs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">flush</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">@@ -689,7 +690,7 @@ def probsFromFile(opts, lastalArgs, codonMatches, lines):</td>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frameshiftProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">codonMatProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">gapCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxGapGrowProb</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matProbsFromCounts</span><span class="p">(</span><span class="n" style="color: #333;">matCounts</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"></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">@@ -779,6 +780,9 @@ def doTraining(opts, args):</td>
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"> <span class="n" style="color: #333;">outerScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># minimum possible (integer) gap extend cost = 1</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"> <span class="n" style="color: #333;">maxGapGrowProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</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="n" style="color: #333;">outerScale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">innerScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outerScale</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaleIncrease</span></span>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"> <span class="n" style="color: #333;">oldParameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"></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">@@ -789,8 +793,8 @@ def doTraining(opts, args):</td>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initialCodonProbs</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">codonMatches</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="python"> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">maxGapGrowProb</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">codonMatches</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="python"> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapRatiosFunc</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gapProbs</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">@@ -801,7 +805,7 @@ def doTraining(opts, args):</td>
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python"> <span class="n" style="color: #333;">rowProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">freqText</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">]</span></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"> <span class="n" style="color: #333;">colProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">freqText</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">colProbs</span><span class="p">]</span></span>
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="python"> <span class="n" style="color: #333;">matParams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchRatio</span><span class="p">,</span> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">rowProbs</span><span class="p">,</span> <span class="n" style="color: #333;">colProbs</span></span>
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804
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScaleFunc</span><span class="p">(</span><span class="n" style="color: #333;">innerScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScaleFunc</span><span class="p">(</span><span class="n" style="color: #333;">innerScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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805
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ss</span></span>
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806
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"> <span class="n" style="color: #333;">writeGapCosts</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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807
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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">@@ -827,10 +831,10 @@ def doTraining(opts, args):</td>
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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828
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">codon</span><span class="p">:</span></span>
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">proc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastSplitProcess</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">proc</span><span class="p">)</span></span>
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830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">codonMatches</span></span><span class="p">,</span></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="python"> <span class="n" style="color: #333;">matProbs</span><span class="p">,</span> <span class="n" style="color: #333;">gapProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">lastalArgs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">maxGapGrowProb</span></span><span class="p">,</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">codonMatches</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">proc</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScaleFunc</span><span class="p">(</span><span class="n" style="color: #333;">outerScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scoresAndScaleFunc</span><span class="p">(</span><span class="n" style="color: #333;">outerScale</span><span class="p">,</span> <span class="n" style="color: #333;">matParams</span><span class="p">,</span> <span class="n" style="color: #333;">delRatios</span><span class="p">,</span> <span class="n" style="color: #333;">insRatios</span><span class="p">)</span></span>
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">matScores</span><span class="p">,</span> <span class="n" style="color: #333;">delCosts</span><span class="p">,</span> <span class="n" style="color: #333;">insCosts</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ss</span></span>
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -X"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">X</span><span class="p">)</span></span>
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">R</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"#last -R"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">R</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">@@ -294,22 +294,20 @@ The result so far is asymmetric: each part of the chimp genome is</td>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="plaintext">aligned to at most one part of the human genome, but not vice-versa.</span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="plaintext">We can get one-to-one alignments like this::</span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext"> <span class="idiff left">maf-swap</span> humchi1.maf | last-<span class="idiff right">split</span> > humchi2.maf</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> <span class="idiff left">last-split -r -m1e-5</span> humchi1.maf | last-<span class="idiff right">postmask</span> > humchi2.maf</span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext">Here, last-split_ gets parts of the humchi1 alignments. It uses the</span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="plaintext">humchi1 *per-base* mismap probabilities to get the humchi2</span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="plaintext">*per-alignment* mismap probabilities.</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">Here, last-split_ gets parts of the humchi1 alignments. The ``-r``</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">reverses the roles of the genomes, so it finds a unique best alignment</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">for each part of human. It uses the humchi1 *per-base* mismap</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">probabilities to get the humchi2 *per-alignment* mismap probabilities.</span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext">Then we can discard less-confident alignments, and convert_ to a</span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="plaintext">compact tabular format::</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">Here we've also discarded less-confident alignments: ``-m1e-5`` omits</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">alignments with `mismap probability`_ > 10^-5, and last-postmask_</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">discards alignments caused by simple sequence.</span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="plaintext"> last-postmask humchi2.maf | maf-convert -n tab | awk -F= '$2 <= 1e-5' > humchi.tab</span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="plaintext">last-postmask_ discards alignments caused by simple sequence. The</span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext">``awk`` command gets alignments with `mismap probability`_ ≤ 10^-5.</span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext">Finally, we can make a dotplot_::</span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="plaintext"> last-dotplot humchi<span class="idiff left right">.tab</span> humchi.png</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> last-dotplot humchi<span class="idiff left">2.maf</span> humchi<span class="idiff right">2</span>.png</span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext">**To go faster** with minor accuracy loss: replace ``-uNEAR`` with</span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="plaintext">``-uRY32`` and/or `mask repeats`_.</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">@@ -404,7 +402,6 @@ core is indicated by "~" symbols, and it contains exact matches only.</td>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="plaintext">.. _mismap probability:</span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext">.. _last-split: doc/last-split.rst</span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext">.. _last-train: doc/last-train.rst</span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="plaintext">.. _convert:</span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext">.. _maf-convert: doc/maf-convert.rst</span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext">.. _scoring scheme: doc/last-matrices.rst</span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="plaintext">.. _seeding scheme:</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#e6aa9861192a0b058083f4ef525daf93befa49e4"><strong>doc/last-split.rst</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">@@ -177,6 +177,11 @@ Options</td>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> alignments have "p" lines from ``lastal -j``, in which case</span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"> the default is ``MAF+``).</span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">-r, --reverse</span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> Reverse the roles of the 2 sequences in each alignment: use the</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> 1st (top) sequence as the "query" and the 2nd as the</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> "reference".</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext">-g, --genome=NAME</span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"> Do spliced alignment, and read splice signals (GT, AG, etc)</span>
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="plaintext"> from the named genome. NAME should be the name of a lastdb</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">@@ -288,6 +293,7 @@ Limitations</td>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="plaintext">last-split does not support:</span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">* DNA-versus-protein alignments.</span>
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291
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="plaintext">* Generalized affine gap costs.</span>
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292
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="plaintext">To do</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#5e55dbeefff2057b414960d9467d183920e31b8a"><strong>src/Alignment.cc</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">@@ -12,20 +12,6 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addExpectedCounts</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">totalCounts</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpectedCount</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ec</span><span class="p">)</span> <span class="p">{</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</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="LC17" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</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="LC18" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">totalCounts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">totalCounts</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">totalCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">totalCounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// deleted letter count</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">totalCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// inserted letter count</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">totalCounts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// deletion open/close count</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">totalCounts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ec</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// insertion open/close count</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addSeedCounts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">counts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</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">@@ -291,6 +277,15 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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291
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">aligner</span><span class="p">();</span></span>
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292
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">GreedyXdropAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">greedyAligner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligners</span><span class="p">.</span><span class="n" style="color: #333;">greedyAligner</span><span class="p">;</span></span>
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293
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranCounts</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</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="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">subsCounts</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;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">frameSize</span> <span class="p">){</span></span>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isGreedy</span> <span class="p">);</span></span>
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">globality</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="323" style="width: 35px; color: rgba(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="318" style="width: 35px; color: rgba(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">@@ -323,14 +318,7 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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323
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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324
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">);</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">getColumnCodes</span><span class="p">(</span><span class="n" style="color: #333;">fxa</span><span class="p">,</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span> <span class="n" style="color: #333;">chunks</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">subsCounts</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</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="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">subsCounts</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;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tranCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">subsCounts</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="n" style="color: #333;">fxa</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">subsCounts</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <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="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isFullScore</span><span class="p">);</span></span>
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</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">@@ -429,17 +417,15 @@ void Alignment::extend( std::vector< SegmentPair >& chunks,</td>
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429
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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430
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="p">}</span></span>
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431
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">seq1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// gamma-centroid / LAMA alignment</span></span>
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">dp</span><span class="p">(</span><span class="n" style="color: #333;">outputType</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">);</span></span>
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435
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">traceback</span><span class="p">(</span><span class="n" style="color: #333;">chunks</span><span class="p">,</span> <span class="n" style="color: #333;">outputType</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">);</span></span>
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"> <span class="p">}</span></span>
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">getColumnCodes</span><span class="p">(</span><span class="n" style="color: #333;">centroid</span><span class="p">,</span> <span class="n" style="color: #333;">columnCodes</span><span class="p">,</span> <span class="n" style="color: #333;">chunks</span><span class="p">,</span> <span class="n" style="color: #333;">isForward</span><span class="p">);</span></span>
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438
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpectedCount</span> <span class="n" style="color: #333;">ec</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">computeExpectedCounts</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="n" style="color: #333;">isForward</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">ec</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;">addExpectedCounts</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">expectedCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ec</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">addExpectedCounts</span><span class="p">(</span><span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="n" style="color: #333;">isForward</span><span class="p">,</span> <span class="n" style="color: #333;">probMat</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">subsCounts</span><span class="p">,</span> <span class="n" style="color: #333;">tranCounts</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#76a46dca9f85ee73b2a8d67a89f4b9bf80c34b4b"><strong>src/Centroid.cc</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">@@ -5,7 +5,6 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GappedXdropAlignerInl.hh"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cassert></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath> // for exp</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cfloat> // for DBL_MAX</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></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">@@ -19,19 +18,6 @@ namespace{</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpectedCount</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExpectedCount</span> <span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d0</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="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">toMatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">][</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setPssm</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pssm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">qsize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">T</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">OneQualityExpMatrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">oqem</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequenceBeg</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualityBeg</span> <span class="p">)</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">@@ -83,255 +69,239 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initForwardMatrix</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span> <span class="n" style="color: #333;">numAntidiagonals</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">fM</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">fM</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span> <span class="n" style="color: #333;">n</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">fD</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span> <span class="n" style="color: #333;">n</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">fI</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span> <span class="n" style="color: #333;">n</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">fM</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initBackwardMatrix</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span> <span class="n" style="color: #333;">numAntidiagonals</span> <span class="p">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">bM</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">bD</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">bI</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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105
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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106
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pssmExp</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</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;">pssmExp2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2</span><span class="p">;</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">pssmPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pssmExp</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</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;">pssmExp2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">;</span></span>
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108
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">numAntidiagonals</span><span class="p">();</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">initForwardMatrix</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// partion function of forward values</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// loop over antidiagonals</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// sum of forward values</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledDelNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledInsNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">initForward</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">hori</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">vert</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">diag</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span> <span class="n" style="color: #333;">horiBeg</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span> <span class="n" style="color: #333;">vertBeg</span> <span class="p">];</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span> <span class="n" style="color: #333;">diagBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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141
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">fM0last</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">fM0</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">xa</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">numCellsAndPads</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uchar</span></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">s1</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">isExtendFwd</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">seq1</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">seq1beg</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">seq1</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">seq1beg</span></span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sumOfEdgeProbRatios</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">0</span></span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">logSumOfProbRatios</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">0</span></span><span class="p">;</span></span>
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145
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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146
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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147
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM0</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD0</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI0</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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148
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="p">}</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <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;">pssm</span><span class="p">)</span> <span class="p">{</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">][</span><span class="n" style="color: #333;">letter2</span><span class="p">];</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM2</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD1</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI1</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledDelNext</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledInsNext</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_f</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fM0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">fM0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">fM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</span><span class="p">];</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span><span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nextPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1ptr</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <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;">pssmPtr</span><span class="p">)</span> <span class="p">{</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2ptr</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fD1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fI1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fM2</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;">xD</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">fD0</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;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">fI0</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;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">fM0</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;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <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="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matchProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchProbs</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledDelNext</span><span class="p">;</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledInsNext</span><span class="p">;</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_f</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fM0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">fM0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI0</span><span class="o" style="font-weight: 600;">++</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="cpp"> <span class="n" style="color: #333;">fM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pssmPtr</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span><span class="p">)[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">];</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fD1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fI1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fM2</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;">xD</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span><span class="p">;</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">fD0</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;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">fI0</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;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">fM0</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;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span><span class="p">;</span></span>
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197
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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198
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <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;">globality</span> <span class="p">)</span> <span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sum_f</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">sum_f</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// seems ugly</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// scaling</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// k</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2ptr</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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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfEdgeProbRatios</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fM2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fD1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fI1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">)][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfEdgeProbRatios</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fM2</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;">fD1</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;">fI1</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="p">}</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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206
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "# Z=" << Z << std::endl;</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">Z</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span> <span class="p">);</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span><span class="p">[</span> <span class="n" style="color: #333;">numAntidiagonals</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;">Z</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// this causes scaled Z to equal 1</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">logPartitionFunction</span><span class="p">();</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">horiPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextPos</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">newSeq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newSeq1beg</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)</span> <span class="p">{</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newSeq1beg</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diagPos</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">horiPos</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pssmPtr</span><span class="p">)</span> <span class="n" style="color: #333;">pssmPtr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="p">}</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rescaleStep</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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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</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="n" style="color: #333;">sumOfProbRatios</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">rescales</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</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;">scale</span><span class="p">;</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">rescaleFwdProbs</span><span class="p">(</span><span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">thisPos</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">logSumOfProbRatios</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">sumOfProbRatios</span><span class="p">);</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfEdgeProbRatios</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="p">}</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">sumOfEdgeProbRatios</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="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumOfEdgeProbRatios</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="p">}</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">rescaledSumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumOfProbRatios</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">logSumOfProbRatios</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">sumOfProbRatios</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// added by M. Hamada</span></span>
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// compute posterior probabilities while executing backward algorithm</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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217
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pssmExp</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</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;">pssmExp2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">mD</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">mI</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">initBackwardMatrix</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledUnit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">--</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">scaledUnit</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledDelNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledInsNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bI</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">hori</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">vert</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">diag</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</span><span class="p">[</span> <span class="n" style="color: #333;">horiBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bI</span><span class="p">[</span> <span class="n" style="color: #333;">vertBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</span><span class="p">[</span> <span class="n" style="color: #333;">diagBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span> <span class="n" style="color: #333;">horiBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span> <span class="n" style="color: #333;">vertBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM0last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">numCellsAndPads</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mDout</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mD</span><span class="p">[</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mIout</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mI</span><span class="p">[</span> <span class="n" style="color: #333;">seq2pos</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <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;">pssm</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">][</span><span class="n" style="color: #333;">letter2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">oldPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</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="cpp"> <span class="n" style="color: #333;">initBackward</span><span class="p">(</span><span class="n" style="color: #333;">oldPos</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scaledUnit</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="n" style="color: #333;">rescaledSumOfProbRatios</span><span class="p">;</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</span><span class="p">[</span><span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">];</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</span><span class="p">[</span><span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">];</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bI</span><span class="p">[</span><span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">];</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span><span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">];</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span><span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">];</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">vert</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">);</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">);</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</span><span class="p">[</span><span class="n" style="color: #333;">vertPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bI</span><span class="p">[</span><span class="n" style="color: #333;">vertPos</span><span class="p">];</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</span><span class="p">[</span><span class="n" style="color: #333;">diagPos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mDout</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mD</span><span class="p">[</span><span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mIout</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mI</span><span class="p">[</span><span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1ptr</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// !!! careful: values written into pad cells may be wrong</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// !!! (overwrite each other, wrong scaling)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <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;">pssmPtr</span><span class="p">)</span> <span class="p">{</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2ptr</span><span class="p">;</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">];</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bM0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bD0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bI0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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276
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <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;">globality</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">scaledUnit</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// xxx matchProb should be 0 only at delimiters, but will be</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 0 for non-delimiters with severe mismatch scores</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledDelNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledInsNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">bM2</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;">ySum</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">bD1</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;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">bI1</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;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mDout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">fD1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">bD1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mIout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">fI1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">bI1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mDout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left">fD0</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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">yD</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mIout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left">fI0</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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">yI</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bM0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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292
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">mDout</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">mIout</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">bM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">bM0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bD0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bI0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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296
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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297
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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298
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="p">}</span></span>
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299
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span><span class="p">)[</span><span class="n" style="color: #333;">letter1</span><span class="p">];</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM0</span><span class="p">;</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD0</span><span class="p">;</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI0</span><span class="p">;</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pssmPtr</span><span class="p">;</span></span>
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309
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span><span class="p">)[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">];</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bM0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bD0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bI0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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310
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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311
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"></span>
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312
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <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;">globality</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">scaledUnit</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx</span></span>
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313
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale2</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledDelNext</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scaledInsNext</span><span class="p">;</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">bM2</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;">ySum</span><span class="p">;</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">bD1</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;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">bI1</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;">ySum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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319
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mDout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">fD1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">bD1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mIout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">fI1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">bI1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mDout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left">fD0</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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">yD</span></span><span class="p">;</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mIout</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff left">fI0</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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">yI</span></span><span class="p">;</span></span>
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322
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bM0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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324
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">mDout</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">mIout</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">bM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">bM0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bD0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bI0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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328
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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329
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="p">}</span></span>
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331
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "# bM[0]=" << bM[0] << std::endl;</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">oldPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newPos</span><span class="p">;</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rescaleStep</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>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">)</span> <span class="p">{</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rescales</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">];</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">rescaleBckProbs</span><span class="p">(</span><span class="n" style="color: #333;">diagPos</span><span class="p">,</span> <span class="n" style="color: #333;">newPos</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">);</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">scaledUnit</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="p">}</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">newSeq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newSeq1beg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)</span> <span class="p">{</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newSeq1beg</span><span class="p">;</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1ptr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2ptr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pssmPtr</span><span class="p">)</span> <span class="n" style="color: #333;">pssmPtr</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"></span>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dp_centroid</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gamma</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">@@ -510,14 +480,6 @@ namespace cbrc{</td>
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510
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">ambiguityCodes</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">asciiProbability</span><span class="p">(</span><span class="n" style="color: #333;">mI</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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511
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cpp"> <span class="p">}</span></span>
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512
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">logPartitionFunction</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log</span><span class="p">(</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">countUncertainLetters</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">counts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignProb</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probRatios</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">@@ -537,14 +499,12 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">computeExpectedCounts</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpectedCount</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pssmExp</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</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;">pssmExp2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Centroid</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addExpectedCounts</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionCounts</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">transitionCounts</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">letterProbs</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="LC509" class="line" lang="cpp"> <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;">letterProbsPerPosition</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">letterProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">letterProbsPerPosition</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabetSize</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">@@ -554,114 +514,98 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alphabetSizeIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> <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;">isExtendFwd</span><span class="p">)</span> <span class="n" style="color: #333;">alphabetSizeIncrement</span> <span class="o" style="font-weight: 600;">*=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNextCount</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="LC558" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNextCount</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="LC517" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</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="LC518" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</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="LC519" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xdropPadLen</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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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// loop over antidiagonals</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignedLetterPairCount</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="LC523" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNextCount</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="LC524" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNextCount</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="LC525" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bI</span><span class="p">[</span> <span class="n" style="color: #333;">scoreEnd</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">hori</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">vert</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">diag</span><span class="p">(</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">seq1beg</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span> <span class="n" style="color: #333;">horiBeg</span> <span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span> <span class="n" style="color: #333;">vertBeg</span> <span class="p">];</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fM2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span> <span class="n" style="color: #333;">diagBeg</span> <span class="p">];</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bM</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bD</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bI</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM0</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fM</span><span class="p">[</span><span class="n" style="color: #333;">thisPos</span><span class="p">];</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fD</span><span class="p">[</span><span class="n" style="color: #333;">vertPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fI</span><span class="p">[</span><span class="n" style="color: #333;">vertPos</span><span class="p">];</span></span>
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577
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"></span>
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dNextCount</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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579
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">iNextCount</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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580
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cpp"></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bM0last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">numCellsAndPads</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp"></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq1beg</span><span class="p">;</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp"> <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;">pssm</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">][</span><span class="n" style="color: #333;">letter2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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603
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">][</span><span class="n" style="color: #333;">letter2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="cpp"> <span class="n" style="color: #333;">delInitCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yD</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="cpp"> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yD</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">insInitCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yI</span><span class="p">;</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="cpp"> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yI</span><span class="p">;</span></span>
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609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="cpp"></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bM0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">fM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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612
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="cpp"> <span class="n" style="color: #333;">bM0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bD0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bI0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">;</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nextPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1ptr</span><span class="p">;</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <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;">letterProbs</span><span class="p">)</span> <span class="p">{</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2ptr</span><span class="p">;</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fM0</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;">bM0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="n" style="color: #333;">substitutionCounts</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">alignedLetterPairCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fD1</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;">bD0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fI1</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;">bI0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="cpp"> <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="LC617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq2pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2pos</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabetSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lp2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isExtendFwd</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">letterProbs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">letterProbs</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// inner most loop</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lp2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">letterProbs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fM0</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;">bM0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">letter1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p2</span><span class="p">)[</span><span class="n" style="color: #333;">letter1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bM0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bD0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bI0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fM2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fD1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fI1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">xM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xI</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alignProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yM</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matchProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">countUncertainLetters</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">],</span> <span class="n" style="color: #333;">alignProb</span><span class="p">,</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">countUncertainLetters</span><span class="p">(</span><span class="n" style="color: #333;">substitutionCounts</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">],</span> <span class="n" style="color: #333;">alignProb</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp"> <span class="n" style="color: #333;">alphabetSize</span><span class="p">,</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="n" style="color: #333;">letter1</span><span class="p">],</span> <span class="n" style="color: #333;">lp2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">toMatch</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">delInitCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yD</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xD</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yD</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">insInitCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xSum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yI</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">xI</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yI</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bM0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bM0last</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">fM2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fD1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">fI1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp"> <span class="n" style="color: #333;">bM0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bD0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="n" style="color: #333;">bI0</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">alignedLetterPairCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignProb</span><span class="p">;</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fD1</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;">bD0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fI1</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;">bI0</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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646
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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647
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="cpp"> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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648
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"> <span class="n" style="color: #333;">lp2</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">alphabetSizeIncrement</span><span class="p">;</span></span>
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649
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"> <span class="p">}</span></span>
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650
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"> <span class="p">}</span></span>
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651
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"></span>
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652
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp"> <span class="n" style="color: #333;">delNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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653
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"> <span class="n" style="color: #333;">insNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scale1</span><span class="p">;</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">antidiagonal</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;">rescaleStep</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>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">antidiagonal</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="n" style="color: #333;">numAntidiagonals</span><span class="p">)</span> <span class="p">{</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mul</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rescales</span><span class="p">[</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">];</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="n" style="color: #333;">dNextCount</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="n" style="color: #333;">iNextCount</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">mul</span><span class="p">;</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="p">}</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">delNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dNextCount</span><span class="p">;</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">insNextCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">iNextCount</span><span class="p">;</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">numAntidiagonals</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"> <span class="n" style="color: #333;">vertPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xdropPadLen</span><span class="p">;</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">newSeq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">seq1start</span><span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span><span class="p">);</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">newSeq1beg</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq1beg</span><span class="p">)</span> <span class="p">{</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newSeq1beg</span><span class="p">;</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vertPos</span><span class="p">;</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">;</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">letterProbs</span><span class="p">)</span> <span class="n" style="color: #333;">letterProbs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alphabetSizeIncrement</span><span class="p">;</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="p">}</span></span>
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cpp"></span>
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656
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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658
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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659
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delCount</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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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insCount</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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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="n" style="color: #333;">delCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mD</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="n" style="color: #333;">insCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mI</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="n" style="color: #333;">delNextCount</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> <span class="n" style="color: #333;">insNextCount</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">growProb</span><span class="p">;</span></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">delInit</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">delInitCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">delNext</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">delNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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663
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">insInit</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insInitCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">insNext</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insNextCount</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alignedLetterPairCount</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">delCount</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// deleted letter count</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insCount</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// inserted letter count</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">delCount</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">delNextCount</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// delete open/close count</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="n" style="color: #333;">transitionCounts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insCount</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">insNextCount</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// insert open/close count</span></span>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// end namespace cbrc</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">@@ -18,24 +18,15 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">ExpectedCount</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">emit</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">][</span><span class="n" style="color: #333;">scoreMatrixRowSize</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">toMatch</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insNext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpectedCount</span> <span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * (1) Forward and backward algorithm on the DP region given by Xdrop algorithm</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * (2) \gamma-centroid decoding</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Centroid</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">const_dbl_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dbl_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">rescaleStep</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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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="nl">public:</span></span>
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41
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">GappedXdropAligner</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aligner</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xa</span><span class="p">;</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">@@ -63,8 +54,7 @@ namespace cbrc{</td>
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63
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">backward</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isExtendFwd</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">globality</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></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">@@ -101,11 +91,11 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq2beg</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Added by MH (2008/10/10) : compute expected counts for transitions and emissions</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;"><span class="idiff left">compute</span>ExpectedCounts</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uchar</span></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">seq1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uchar</span></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">seq2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isExtendFwd</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff">const_dbl_ptr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">substitutionProbs</span></span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff">GapCosts</span></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">gapCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alphabetSize</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ExpectedCount</span></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">count</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">const</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;"><span class="idiff left">add</span>ExpectedCounts</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isExtendFwd</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">const_dbl_ptr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">substitutionProbs</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">GapCosts</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">gapCosts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alphabetSize</span></span><span class="p">,</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">dbl_ptr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">substitutionCounts</span></span><span class="p">,</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">transitionCounts</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="nl">private:</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ExpMatrixRow</span><span class="p">[</span><span class="n" style="color: #333;">scoreMatrixRowSize</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">@@ -135,16 +125,58 @@ namespace cbrc{</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">dvec_t</span> <span class="n" style="color: #333;">X</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// DP tables for $gamma$-decoding</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">dvec_t</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// scale[n] is a scaling factor for the n-th anti-diagonal</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">dvec_t</span> <span class="n" style="color: #333;">rescales</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rescaledSumOfProbRatios</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq1ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq2ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExpMatrixRow</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pssmPtr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestAntiDiagonal</span><span class="p">;</span></span>
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142
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestPos1</span><span class="p">;</span></span>
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143
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initForwardMatrix</span><span class="p">();</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initBackwardMatrix</span><span class="p">();</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initForward</span><span class="p">()</span> <span class="p">{</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">numAntidiagonals</span><span class="p">();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</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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146
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">logPartitionFunction</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// a.k.a. full score, forward score</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">totalNumOfCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xa</span><span class="p">.</span><span class="n" style="color: #333;">scoreEndIndex</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fM</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">totalNumOfCells</span><span class="p">)</span> <span class="p">{</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">fM</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">totalNumOfCells</span><span class="p">);</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">fD</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">totalNumOfCells</span><span class="p">);</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">fI</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">totalNumOfCells</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">fM</span><span class="p">[</span><span class="n" style="color: #333;">xdropPadLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfRescales</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</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;">rescaleStep</span><span class="p">;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rescales</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfRescales</span><span class="p">)</span> <span class="n" style="color: #333;">rescales</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">numOfRescales</span><span class="p">);</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initBackward</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">totalNumOfCells</span><span class="p">)</span> <span class="p">{</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">bM</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">totalNumOfCells</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">bD</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">totalNumOfCells</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">bI</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">totalNumOfCells</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">mD</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">mI</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">numAntidiagonals</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">rescaleFwdProbs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="p">{</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">fM</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;">scale</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">fD</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;">scale</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">fI</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;">scale</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="p">}</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="p">}</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">rescaleBckProbs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span><span class="p">)</span> <span class="p">{</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">bM</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;">scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">bD</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;">scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">bI</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;">scale</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="p">}</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">updateScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antiDiagonal</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">cur</span><span class="p">)</span> <span class="p">{</span></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <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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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</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">@@ -619,8 +619,10 @@ void LastalArguments::writeCommented( std::ostream& stream ) const{</td>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" B="</span><span class="p">;</span> <span class="n" style="color: #333;">writeIntList</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">insGrowCosts</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">gapPairCost</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="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" c="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gapPairCost</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">isTranslated</span><span class="p">()</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" F="</span><span class="p">;</span> <span class="n" style="color: #333;">writeIntList</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isTranslated</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" F="</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">writeIntList</span><span class="p">(</span><span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="n" style="color: #333;">frameshiftCosts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" e="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minScoreGapped</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" d="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">minScoreGapless</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" x="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">maxDropGapped</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">@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make"> ../build/mat-inc.sh ../data/<span class="k" style="font-weight: 600;">*</span>.mat <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION1</span> <span class="o" style="font-weight: 600;">=</span> git describe <span class="nt" style="color: #000080;">--dirty</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 12<span class="idiff left right">19</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 12<span class="idiff left right">43, refs/keep-around/3243658001e5a2afe5329f23aab272c355465293</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-e</span> ../.git <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(VERSION1)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$(VERSION2)</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#2bf93e35d0ba974fe4be041c601814d14b253461"><strong>src/split/cbrc_unsplit_alignment.cc</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">@@ -142,12 +142,13 @@ void flipMafStrands(StringIt linesBeg, StringIt linesEnd) {</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">canonicalizeMafStrands</span><span class="p">(</span><span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesBeg</span><span class="p">,</span> <span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">canonicalizeMafStrands</span><span class="p">(</span><span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesBeg</span><span class="p">,</span> <span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">rankOfQrySeq</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">s</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="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">linesBeg</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">rankOfQrySeq</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">strand</span><span class="p">;</span></span>
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152
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skipWord</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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153
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skipWord</span><span class="p">(</span><span class="n" style="color: #333;">c</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">@@ -162,8 +163,11 @@ static void canonicalizeMafStrands(StringIt linesBeg, StringIt linesEnd) {</td>
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162
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="s" style="color: #d14;">"bad MAF data"</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UnsplitAlignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">canonicalizeMafStrands</span><span class="p">(</span><span class="n" style="color: #333;">linesBeg</span><span class="p">,</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UnsplitAlignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">rankOfQrySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">rankOfRefSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isTopSeqQuery</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">canonicalizeMafStrands</span><span class="p">(</span><span class="n" style="color: #333;">linesBeg</span><span class="p">,</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">,</span> <span class="n" style="color: #333;">rankOfQrySeq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">qQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// in case the input lacks sequence quality data</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(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">@@ -189,13 +193,13 @@ void UnsplitAlignment::init() {</td>
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189
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <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;">f</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">g</span><span class="p">)</span> <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="s" style="color: #d14;">"bad MAF line: "</span> <span class="o" style="font-weight: 600;">+</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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190
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">)[</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</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="c1" style="color: #998; font-style: italic;">// write a terminator for the sequence name</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lineEnd</span><span class="p">)</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">)[</span><span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</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="c1" style="color: #998; font-style: italic;">// trim trailing whitespace</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">rankOfRefSeq</span></span><span class="p">)</span> <span class="p">{</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">rstart</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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194
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">rend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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195
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">qstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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196
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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197
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">ralign</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cpp"> <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;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <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;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">rankOfQrySeq</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">qstart</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="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">qend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="n" style="color: #333;">qstrand</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qstrand</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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" style="width: 35px; color: rgba(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">@@ -203,9 +207,9 @@ void UnsplitAlignment::init() {</td>
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203
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">qalign</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'q'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">rankOfRefSeq</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="s" style="color: #d14;">"I can't handle quality data for the genomic sequence"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">rankOfQrySeq</span></span><span class="p">)</span> <span class="p">{</span></span>
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209
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skipSpace</span><span class="p">(</span><span class="n" style="color: #333;">skipWord</span><span class="p">(</span><span class="n" style="color: #333;">skipWord</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)));</span></span>
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210
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <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;">f</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">g</span><span class="p">)</span> <span class="n" style="color: #333;">err</span><span class="p">(</span><span class="s" style="color: #d14;">"bad MAF line: "</span> <span class="o" style="font-weight: 600;">+</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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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lineEnd</span><span class="p">)</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">)[</span><span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c</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="c1" style="color: #998; font-style: italic;">// trim trailing whitespace</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#fc998af53d94055438c79cc84b23acd0ff926b3f"><strong>src/split/cbrc_unsplit_alignment.hh</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">@@ -31,9 +31,10 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">qalign</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</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;">qQual</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">UnsplitAlignment</span><span class="p">(){}</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">UnsplitAlignment</span><span class="p">(</span><span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesBegIn</span><span class="p">,</span> <span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesEndIn</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">linesBeg</span><span class="p">(</span><span class="n" style="color: #333;">linesBegIn</span><span class="p">),</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">(</span><span class="n" style="color: #333;">linesEndIn</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">init</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">UnsplitAlignment</span><span class="p">(</span><span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesBegIn</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">StringIt</span> <span class="n" style="color: #333;">linesEndIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">linesBeg</span><span class="p">(</span><span class="n" style="color: #333;">linesBegIn</span><span class="p">),</span> <span class="n" style="color: #333;">linesEnd</span><span class="p">(</span><span class="n" style="color: #333;">linesEndIn</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isForwardStrand</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qstrand</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isFlipped</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qstrand</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="p">};</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#a966121261c9a9a0627d40ae5e6f8274fe2ecc88"><strong>src/split/last-split-main.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,6 +36,7 @@ static void run(int argc, char* argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">LastSplitOptions</span> <span class="n" style="color: #333;">opts</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">format</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="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isTopSeqQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">cis</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.004</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">trans</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1e-05</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +63,7 @@ come from different parts of the genome.\n\</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="s" style="color: #d14;">Options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="s" style="color: #d14;"> -h, --help show this help message and exit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="s" style="color: #d14;"> -f, --format=FMT output format: MAF, MAF+ (default: depends on input)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="s" style="color: #d14;"> -r, --reverse reverse the roles of the 2 sequences in each alignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="s" style="color: #d14;"> -g, --genome=NAME lastdb genome name</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="s" style="color: #d14;"> -d, --direction=D RNA direction: 0=reverse, 1=forward, 2=mixed (default="</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">direction</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,11 +84,12 @@ Options:\n\</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="s" style="color: #d14;"> -V, --version show version information and exit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">sOpts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"hf:g:d:c:t:M:S:m:s:nb:vV"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">sOpts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"hf:<span class="idiff left right">r</span>g:d:c:t:M:S:m:s:nb:vV"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">option</span> <span class="n" style="color: #333;">lOpts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"format"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'f'</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"reverse"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'r'</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"genome"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"direction"</span><span class="p">,</span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'d'</span> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"cis"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'c'</span> <span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,6 +114,9 @@ Options:\n\</td>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span></span>
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112
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseOutputFormat</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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113
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'r'</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isTopSeqQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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114
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">:</span></span>
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isSplicedAlignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#cff6a16c49a626871ebb6399a31650f25e4f5395"><strong>src/split/last-split.cc</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">@@ -51,6 +51,19 @@ static int scoreFromProb(double prob, double scale) {</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">floor</span><span class="p">(</span><span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">prob</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">0.5</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">transpose</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrix</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">m</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cols</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rows</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Defines an ordering, for sorting.</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">less</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UnsplitAlignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UnsplitAlignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="266" style="width: 35px; color: rgba(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">@@ -253,7 +266,8 @@ static void doOneBatch(std::vector<std::string>& mafLines,</td>
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253
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">mafs</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">mafEnds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// saves memory: no excess capacity</span></span>
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254
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mafEnds</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</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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255
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">mafs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UnsplitAlignment</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mafEnds</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mafEnds</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mafEnds</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">));</span></span>
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257
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"></span>
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258
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">mafs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">mafs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">less</span><span class="p">);</span></span>
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259
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cbrc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UnsplitAlignment</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mafs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" style="width: 35px; color: rgba(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="333" style="width: 35px; color: rgba(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">@@ -319,7 +333,8 @@ void lastSplit(LastSplitOptions& opts) {</td>
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319
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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320
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">ls</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">word</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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321
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">ls</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;">row</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">word</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"#"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ls</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">())</span> <span class="p">{</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">word</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"#"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">colNames</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ls</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">())</span> <span class="p">{</span></span>
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323
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">rowNames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>
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324
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">);</span></span>
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325
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <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="375" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -375,6 +390,12 @@ void lastSplit(LastSplitOptions& opts) {</td>
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375
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qualityOffset</span> <span class="o" style="font-weight: 600;">=</span></span>
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376
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">sequenceFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">64</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">33</span><span class="p">;</span></span>
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377
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">printParameters</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">);</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">)</span> <span class="p">{</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">transpose</span><span class="p">(</span><span class="n" style="color: #333;">scoreMatrix</span><span class="p">);</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">rowNames</span><span class="p">,</span> <span class="n" style="color: #333;">colNames</span><span class="p">);</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">gapExistenceCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExistenceCost</span><span class="p">);</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">gapExtensionCost</span><span class="p">,</span> <span class="n" style="color: #333;">insExtensionCost</span><span class="p">);</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="p">}</span></span>
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378
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">sa</span><span class="p">.</span><span class="n" style="color: #333;">setParams</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapExistenceCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gapExtensionCost</span><span class="p">,</span></span>
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379
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExistenceCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insExtensionCost</span><span class="p">,</span></span>
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380
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">jumpCost</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">restartCost</span><span class="p">,</span> <span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">qualityOffset</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="389" style="width: 35px; color: rgba(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="410" style="width: 35px; color: rgba(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">@@ -389,7 +410,7 @@ void lastSplit(LastSplitOptions& opts) {</td>
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389
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="p">}</span></span>
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390
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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391
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// we are reading alignments</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">startsWith</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="s" style="color: #d14;">"# batch"</span><span class="p">))</span> <span class="p">{</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">startsWith</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="s" style="color: #d14;">"# batch"</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">isTopSeqQuery</span></span><span class="p">)</span> <span class="p">{</span></span>
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393
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">addMaf</span><span class="p">(</span><span class="n" style="color: #333;">mafEnds</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">);</span></span>
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394
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">doOneBatch</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">mafEnds</span><span class="p">,</span> <span class="n" style="color: #333;">sa</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">isAlreadySplit</span><span class="p">);</span></span>
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395
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">clear</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">@@ -19,6 +19,7 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">LastSplitOptions</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isTopSeqQuery</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">genome</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">direction</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cis</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#7294d22a62972c98e3d0cae607335ab651731ea8"><strong>test/alli.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>NW_017707804.1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AACACCACAATGAGATACCACCTCACAGCAGTCAGAATGGCTACAATTAA</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">CAAGTCAGGAAAGGACAGAT</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#b9b7e0ba489bbe86e4faf91536af5aadf40107c5"><strong>test/huma.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>57:130722274</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">aaaaccacaatgagagtcagagtggtgattattaaaagtcgagaaatgat</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">agat</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#67a6c42c3d9e350d422617435e9cb54c619cd2e6"><strong>test/last-split-test.out</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">@@ -7,6 +7,7 @@ come from different parts of the genome.</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="">Options:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang=""> -h, --help show this help message and exit</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang=""> -f, --format=FMT output format: MAF, MAF+ (default: depends on input)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang=""> -r, --reverse reverse the roles of the 2 sequences in each alignment</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang=""> -g, --genome=NAME lastdb genome name</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang=""> -d, --direction=D RNA direction: 0=reverse, 1=forward, 2=mixed (default=1)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang=""> -c, --cis=PROB cis-splice probability per base (default=0.004)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43885" style="width: 35px; color: rgba(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="43886" style="width: 35px; color: rgba(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">@@ -43885,3 +43886,80 @@ s chr6 42658730 94 + 170805979 CTGAAATGCA-GCGGCATTTTA--TTGA---TGAAAACAA</td>
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43885
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43886
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<pre style="margin: 0;"> <span id="LC43886" class="line" lang="">s spliceWithGap 2662 98 - 7262 CTGAAATGCATGCAG-ATTTGAGTTTGAGGCTGAAAACAGTGAACT-TTTCAGCAGACATTAGAACTGGATGCCTCAACCTCTGCTGTTCTTGATCATAG</span>
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43886
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43887
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<pre style="margin: 0;"> <span id="LC43887" class="line" lang="">p !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</span>
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43887
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43888
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<pre style="margin: 0;"> <span id="LC43888" class="line" lang=""></span>
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43889
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<pre style="margin: 0;">+<span id="LC43889" class="line" lang="">#</span>
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43890
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<pre style="margin: 0;">+<span id="LC43890" class="line" lang=""># a=31 b=1 A=21 B=3 e=190 d=94 x=189 y=48 z=189 D=1e+09 E=0.516058</span>
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43891
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<pre style="margin: 0;">+<span id="LC43891" class="line" lang=""># R=01 u=0 s=2 S=1 M=0 T=0 m=100 l=1 n=100 k=1 w=1000 t=4.75495 j=3 Q=0</span>
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43892
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<pre style="margin: 0;">+<span id="LC43892" class="line" lang=""># /home/mcfrith/data/genome/calMil1/last/calMil1-uMAM8</span>
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43893
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<pre style="margin: 0;">+<span id="LC43893" class="line" lang=""># Reference sequences=21204 normal letters=936953443</span>
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43894
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<pre style="margin: 0;">+<span id="LC43894" class="line" lang=""># lambda=0.214243 K=0.246122</span>
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43895
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<pre style="margin: 0;">+<span id="LC43895" class="line" lang="">#</span>
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43896
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<pre style="margin: 0;">+<span id="LC43896" class="line" lang=""># A C G T M S K W R Y B D H V</span>
</pre>
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43897
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<pre style="margin: 0;">+<span id="LC43897" class="line" lang=""># A 5 -7 -3 -6 2 -5 -4 2 3 -6 -5 1 1 1</span>
</pre>
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43898
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<pre style="margin: 0;">+<span id="LC43898" class="line" lang=""># C -8 5 -7 -2 2 2 -4 -4 -7 3 1 -5 1 0</span>
</pre>
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43899
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<pre style="margin: 0;">+<span id="LC43899" class="line" lang=""># G -2 -7 5 -8 -4 2 2 -4 3 -7 0 1 -5 1</span>
</pre>
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43900
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<pre style="margin: 0;">+<span id="LC43900" class="line" lang=""># T -6 -3 -7 5 -4 -5 2 2 -6 3 1 1 1 -5</span>
</pre>
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43901
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43901" class="line" lang=""># M 2 2 -5 -4 2 0 -4 0 0 0 -1 -1 1 1</span>
</pre>
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43902
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43902" class="line" lang=""># S -4 2 2 -4 0 2 0 -4 0 0 1 -1 -1 1</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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43903
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43903" class="line" lang=""># K -4 -5 2 2 -4 0 2 0 0 0 1 1 -1 -1</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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43904
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43904" class="line" lang=""># W 2 -5 -5 2 0 -5 0 2 0 0 -1 1 1 -1</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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43905
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43905" class="line" lang=""># R 3 -7 3 -7 0 0 0 0 3 -7 -2 1 -1 1</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="43906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43906
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43906" class="line" lang=""># Y -7 3 -7 3 0 0 0 0 -7 3 1 -1 1 -2</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="43907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43907
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43907" class="line" lang=""># B -5 1 1 1 -1 1 1 -1 -1 1 1 0 0 0</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="43908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43908
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43908" class="line" lang=""># D 1 -5 1 0 -1 -1 1 1 1 -2 -1 1 -1 0</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="43909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43909
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43909" class="line" lang=""># H 0 1 -5 1 1 -1 -1 1 -2 1 0 -1 1 -1</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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43910
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43910" class="line" lang=""># V 1 1 1 -5 1 1 -1 -1 1 -1 0 0 0 1</span>
</pre>
</td>
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43911
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<pre style="margin: 0;">+<span id="LC43911" class="line" lang="">#</span>
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43912
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<pre style="margin: 0;">+<span id="LC43912" class="line" lang=""># Coordinates are 0-based. For - strand matches, coordinates</span>
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<td class="new_line diff-line-num new" data-linenumber="43913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43913
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<pre style="margin: 0;">+<span id="LC43913" class="line" lang=""># in the reverse complement of the 2nd sequence are used.</span>
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43914
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<pre style="margin: 0;">+<span id="LC43914" class="line" lang="">#</span>
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<td class="new_line diff-line-num new" data-linenumber="43915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43915
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<pre style="margin: 0;">+<span id="LC43915" class="line" lang=""># name start alnSize strand seqSize alignment</span>
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43916
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<pre style="margin: 0;">+<span id="LC43916" class="line" lang="">#</span>
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43917
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<pre style="margin: 0;">+<span id="LC43917" class="line" lang=""># m=1 s=190</span>
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43918
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<pre style="margin: 0;">+<span id="LC43918" class="line" lang="">#</span>
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43919
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<pre style="margin: 0;">+<span id="LC43919" class="line" lang=""># Query sequences=195</span>
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43920
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<pre style="margin: 0;">+<span id="LC43920" class="line" lang=""># m=1 s=190</span>
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43921
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<pre style="margin: 0;">+<span id="LC43921" class="line" lang="">#</span>
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43922
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<pre style="margin: 0;">+<span id="LC43922" class="line" lang="">a score=226 mismap=0.2</span>
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43923
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<pre style="margin: 0;">+<span id="LC43923" class="line" lang="">s KI635862 2418202 89 + 12728579 CGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCCGG-ATAACAGGCGCGCGCCACCGCGCCCGGC</span>
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43924
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<pre style="margin: 0;">+<span id="LC43924" class="line" lang="">s chr1 248781029 91 - 248956422 CACTGCAACCTCCACCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGGCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCATGCCCAGC</span>
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43925
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<pre style="margin: 0;">+<span id="LC43925" class="line" lang=""></span>
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43926
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<pre style="margin: 0;">+<span id="LC43926" class="line" lang="">a score=211 mismap=0.5</span>
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43927
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<pre style="margin: 0;">+<span id="LC43927" class="line" lang="">s KI635889 4462115 58 + 6429418 TACCTATAGATTGGTTGACAGCTTTCATGCACAAATTTTCCACCAGAATCTTTCCTGG</span>
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43928
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<pre style="margin: 0;">+<span id="LC43928" class="line" lang="">s chr1 248943367 58 - 248956422 TGCCTATGGACTGGTTGACAGCCTTCATGCACAGGTTCTCCACCAGAGCCTTTCTTGG</span>
</pre>
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43929
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<pre style="margin: 0;">+<span id="LC43929" class="line" lang=""></span>
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<td class="new_line diff-line-num new" data-linenumber="43930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43930
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<pre style="margin: 0;">+<span id="LC43930" class="line" lang="">a score=271 mismap=1.3e-08</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43931
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<pre style="margin: 0;">+<span id="LC43931" class="line" lang="">s KI635901 1311390 127 + 5048387 TCTTTTTTTCCTTCTGTCAACACTTTTAGCTGAAGCCATAAAAACGACAAGTCCCGTCATAATCCCATACCCACTCTTTCAGTCCAATGCTGAAGATCTTAGTGTTGAAGGTTTACCCGAAGGTATT</span>
</pre>
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43932
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<pre style="margin: 0;">+<span id="LC43932" class="line" lang="">s chr1 248791606 123 - 248956422 TCCCTttttctttttttt----CTTATAGCTCGAGCTGTAAAAGCCAAAGGTCCGGTGATGATCCCATACCCTTTTTTCCAGTCTCATGTTGAAGATTTTTATGTAGAAGGCCTtcccaaaggaatt</span>
</pre>
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43933
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<pre style="margin: 0;">+<span id="LC43933" class="line" lang=""></span>
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<td class="new_line diff-line-num new" data-linenumber="43934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43934
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<pre style="margin: 0;">+<span id="LC43934" class="line" lang="">a score=392 mismap=3.2e-06</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="43935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43935
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<pre style="margin: 0;">+<span id="LC43935" class="line" lang="">s KI635917 1140607 159 + 4339253 ACCTTGTTcttgttccttctgcttcttcttcttctccatcttaatcAGCTTTGCATTGCGCAGTTTGGCCTTTCCAATGCCTCCGGCCTGACGAATGGATTCCAGCAGACTAGCCCTTCCATCCGAGGGTTTCACAACCTCCTTGGGTGCCCCCTGGAC</span>
</pre>
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43936
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<pre style="margin: 0;">+<span id="LC43936" class="line" lang="">s chr1 186314 156 + 248956422 ACCTTGCTCctgctccttctg---cttcttcttctccAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTCGACCACTTCCCTGGGAGCTCCCTGGAC</span>
</pre>
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43937
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<pre style="margin: 0;">+<span id="LC43937" class="line" lang=""></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43938
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<pre style="margin: 0;">+<span id="LC43938" class="line" lang="">a score=520 mismap=0.2</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43939
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<pre style="margin: 0;">+<span id="LC43939" class="line" lang="">s KI635917 1143406 188 + 4339253 TCTGTGCTGAACGTGGGCAGTTCAGGCATGTTGCTTCCTGGCACGGAGGGCGCGATGCCAGGTCCCAGGTCAGCACTGTACATGAGGTCATCTGCAATCCCAGGCAGATCCGGTAGGTAGGATGGGACGTCAATCTCTGGGACCTGACCCAGGTCTGGTACATAGAAGTAATTCTCAGTAGTCTGAAA</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43940
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<pre style="margin: 0;">+<span id="LC43940" class="line" lang="">s chr1 16876 185 + 248956422 TCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGC---CAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAA</span>
</pre>
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43941
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<pre style="margin: 0;">+<span id="LC43941" class="line" lang=""></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43942
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<pre style="margin: 0;">+<span id="LC43942" class="line" lang="">a score=340 mismap=1e-09</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="43888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="43943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43943
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<pre style="margin: 0;">+<span id="LC43943" class="line" lang="">s KI635917 1144102 140 + 4339253 ACCCGTCTTTCTAGTTGCTCTCGCGTGGTGATTGAGAGCGGGGCATCAAACGGCTTCTCTTCCTTCTCAGTCTCCAGTGCCATGTGTGTCTTTGTCACAGCTCCTGCTAACGGATCCAAGAGAACGTACTTCTTGTAGCT</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43944
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43944" class="line" lang="">s chr1 17230 140 + 248956422 ACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCT</span>
</pre>
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43945
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<pre style="margin: 0;">+<span id="LC43945" class="line" lang=""></span>
</pre>
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43946
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<pre style="margin: 0;">+<span id="LC43946" class="line" lang="">a score=334 mismap=1e-09</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43947
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<pre style="margin: 0;">+<span id="LC43947" class="line" lang="">s KI635917 1144725 145 + 4339253 TACGGATTCTCAGTAGTGTTGAACAGCAGCAGGGAGCTGATGGAGCTAATGTTCCGAGGAAGGCTTCCCAACCCCTCCTCCGTCTCATCCTCCTCTCGAGACTTGGTGTTCAGACACACGGGGTAATGCTTTGCCTTTTCCTGAG</span>
</pre>
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43948
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<pre style="margin: 0;">+<span id="LC43948" class="line" lang="">s chr1 17602 145 + 248956422 TACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAG</span>
</pre>
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43949
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<pre style="margin: 0;">+<span id="LC43949" class="line" lang=""></span>
</pre>
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43950
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<pre style="margin: 0;">+<span id="LC43950" class="line" lang="">a score=340 mismap=1e-09</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43951
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<pre style="margin: 0;">+<span id="LC43951" class="line" lang="">s KI635917 1146887 159 + 4339253 CACACCTGCACAGCCTTATCATCCAGAGGCTTCAGCTTGCTGTGGATCTTGTAGCGTGGGCGCTTCTGAGAAGCAGGATCATCCGCGCCCGAGAATATGGAAGTGTAATCCTGTAGCCGGTCAGGTGCAGGGTACTTAGCACTGGAAAAGACCTGCAGA</span>
</pre>
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43952
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43952" class="line" lang="">s chr1 17909 159 + 248956422 CAGACCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGA</span>
</pre>
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43953
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<pre style="margin: 0;">+<span id="LC43953" class="line" lang=""></span>
</pre>
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43954
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<pre style="margin: 0;">+<span id="LC43954" class="line" lang="">a score=240 mismap=1.6e-05</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43955
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<pre style="margin: 0;">+<span id="LC43955" class="line" lang="">s KI635917 1147176 117 + 4339253 TACTTTTGTGGCTTTCTTGCTGCCTTTGATCCTCTCGATCTTGGCCTGTGCCAGATTGATGCGGTCACTGATGGACTGCAGGCGAGTCTGATTCCTCTCCACGTTTTGGGAAACCCT</span>
</pre>
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43956
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43956" class="line" lang="">s chr1 18264 117 + 248956422 TACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCT</span>
</pre>
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43957
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<pre style="margin: 0;">+<span id="LC43957" class="line" lang=""></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43958
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<pre style="margin: 0;">+<span id="LC43958" class="line" lang="">a score=252 mismap=1e-06</span>
</pre>
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43959
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<pre style="margin: 0;">+<span id="LC43959" class="line" lang="">s KI635917 1161884 119 + 4339253 ACCTCGTGAAGACATCATTGGAGATTTTTTGGAGATACTGAAGAGCATCAGTGATCTGGTGAATGGACTCTTCCCGGCGCAGGTCCGGCTGGATTATTGGCACCGTGTACACCTGTCCT</span>
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43960
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<pre style="margin: 0;">+<span id="LC43960" class="line" lang="">s chr1 24735 119 + 248956422 ACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCT</span>
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43961
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<pre style="margin: 0;">+<span id="LC43961" class="line" lang=""></span>
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43962
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<pre style="margin: 0;">+<span id="LC43962" class="line" lang="">a score=330 mismap=0.79</span>
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43963
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<pre style="margin: 0;">+<span id="LC43963" class="line" lang="">s KI636063 409336 105 + 789923 AAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCCATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAGCGAGCA</span>
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43964
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<pre style="margin: 0;">+<span id="LC43964" class="line" lang="">s chr1 157784 102 + 248956422 aaaataTGGAATGCTTCACAAATTTGCATGTCATTCTTTCACAGAGGCCGTGCCAA---TCTCTCTATTGTTCCAACTTAAGTATGTGTGCTACTGAGGCAAGCA</span>
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43965
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<pre style="margin: 0;">+<span id="LC43965" class="line" lang=""></span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#ee216b9a6e5260afd4420396b9136119dc88bb38"><strong>test/last-split-test.sh</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">@@ -33,4 +33,7 @@ maf=SRR359290-1k.maf</td>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"> last-split <span class="nt" style="color: #000080;">-fMAF</span> 102.maf</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"> last-split <span class="nt" style="color: #000080;">-d1</span> <span class="nt" style="color: #000080;">-fMAF</span>+ spliceWithGap.maf</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> last-split <span class="nt" style="color: #000080;">-r</span> split1.maf</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> | diff <span class="nt" style="color: #000080;">-u</span> last-split-test.out -</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#6c90adec85ff9834658c43a287e5d780f52732ef"><strong>test/last-test.out</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">@@ -4792,3 +4792,39 @@ s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATA</td>
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4792
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4792
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<pre style="margin: 0;"> <span id="LC4792" class="line" lang="plaintext">140 chrM 3279 28 + 16571 chrM 10177 28 - 16775 28 EG2=1.5e+05 E=8.5e-05</span>
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4793
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4793
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<pre style="margin: 0;"> <span id="LC4793" class="line" lang="plaintext"># batch 1</span>
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4794
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4794
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<pre style="margin: 0;"> <span id="LC4794" class="line" lang="plaintext"># Query sequences=2</span>
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4795
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<pre style="margin: 0;">+<span id="LC4795" class="line" lang="plaintext">#</span>
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4796
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<pre style="margin: 0;">+<span id="LC4796" class="line" lang="plaintext"># a=15 b=3 A=15 B=3 e=79 d=40 x=78 y=46 z=78 D=1e+06 E=1.42772e+10</span>
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4797
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<pre style="margin: 0;">+<span id="LC4797" class="line" lang="plaintext"># R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=4.5512 j=7 Q=0</span>
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4798
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<pre style="margin: 0;">+<span id="LC4798" class="line" lang="plaintext"># /tmp/last-test</span>
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4799
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<pre style="margin: 0;">+<span id="LC4799" class="line" lang="plaintext"># Reference sequences=1 normal letters=70</span>
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<td class="new_line diff-line-num new" data-linenumber="4800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4800
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<pre style="margin: 0;">+<span id="LC4800" class="line" lang="plaintext"># lambda=0.203841 K=0.140698</span>
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<td class="new_line diff-line-num new" data-linenumber="4801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4801
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<pre style="margin: 0;">+<span id="LC4801" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="4802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4802
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<pre style="margin: 0;">+<span id="LC4802" class="line" lang="plaintext"># A C G T M S K W R Y B D H V</span>
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<td class="new_line diff-line-num new" data-linenumber="4803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4803
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<pre style="margin: 0;">+<span id="LC4803" class="line" lang="plaintext"># A 5 -5 -5 -5 2 -5 -5 2 2 -5 -5 1 1 1</span>
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<td class="new_line diff-line-num new" data-linenumber="4804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4804
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<pre style="margin: 0;">+<span id="LC4804" class="line" lang="plaintext"># C -5 5 -5 -5 2 2 -5 -5 -5 2 1 -5 1 1</span>
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<td class="old_line diff-line-num new" data-linenumber="4795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4805
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<pre style="margin: 0;">+<span id="LC4805" class="line" lang="plaintext"># G -5 -5 5 -5 -5 2 2 -5 2 -5 1 1 -5 1</span>
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<td class="new_line diff-line-num new" data-linenumber="4806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4806
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<pre style="margin: 0;">+<span id="LC4806" class="line" lang="plaintext"># T -5 -5 -5 5 -5 -5 2 2 -5 2 1 1 1 -5</span>
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<td class="new_line diff-line-num new" data-linenumber="4807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4807
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<pre style="margin: 0;">+<span id="LC4807" class="line" lang="plaintext"># M 2 2 -5 -5 2 0 -5 0 0 0 -1 -1 1 1</span>
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<td class="new_line diff-line-num new" data-linenumber="4808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4808
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<pre style="margin: 0;">+<span id="LC4808" class="line" lang="plaintext"># S -5 2 2 -5 0 2 0 -5 0 0 1 -1 -1 1</span>
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4809
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<pre style="margin: 0;">+<span id="LC4809" class="line" lang="plaintext"># K -5 -5 2 2 -5 0 2 0 0 0 1 1 -1 -1</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="4795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4810
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<pre style="margin: 0;">+<span id="LC4810" class="line" lang="plaintext"># W 2 -5 -5 2 0 -5 0 2 0 0 -1 1 1 -1</span>
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<td class="new_line diff-line-num new" data-linenumber="4811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4811
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<pre style="margin: 0;">+<span id="LC4811" class="line" lang="plaintext"># R 2 -5 2 -5 0 0 0 0 2 -5 -1 1 -1 1</span>
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<td class="new_line diff-line-num new" data-linenumber="4812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4812
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<pre style="margin: 0;">+<span id="LC4812" class="line" lang="plaintext"># Y -5 2 -5 2 0 0 0 0 -5 2 1 -1 1 -1</span>
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<td class="old_line diff-line-num new" data-linenumber="4795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4813
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<pre style="margin: 0;">+<span id="LC4813" class="line" lang="plaintext"># B -5 1 1 1 -1 1 1 -1 -1 1 1 0 0 0</span>
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<td class="new_line diff-line-num new" data-linenumber="4814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4814
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<pre style="margin: 0;">+<span id="LC4814" class="line" lang="plaintext"># D 1 -5 1 1 -1 -1 1 1 1 -1 0 1 0 0</span>
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<td class="new_line diff-line-num new" data-linenumber="4815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4815
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<pre style="margin: 0;">+<span id="LC4815" class="line" lang="plaintext"># H 1 1 -5 1 1 -1 -1 1 -1 1 0 0 1 0</span>
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<td class="new_line diff-line-num new" data-linenumber="4816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4816
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<pre style="margin: 0;">+<span id="LC4816" class="line" lang="plaintext"># V 1 1 1 -5 1 1 -1 -1 1 -1 0 0 0 1</span>
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4817
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<pre style="margin: 0;">+<span id="LC4817" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="4818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4818
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<pre style="margin: 0;">+<span id="LC4818" class="line" lang="plaintext"># Coordinates are 0-based. For - strand matches, coordinates</span>
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<td class="new_line diff-line-num new" data-linenumber="4819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4819
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<pre style="margin: 0;">+<span id="LC4819" class="line" lang="plaintext"># in the reverse complement of the 2nd sequence are used.</span>
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<td class="new_line diff-line-num new" data-linenumber="4820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4820
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<pre style="margin: 0;">+<span id="LC4820" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="4821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4821
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<pre style="margin: 0;">+<span id="LC4821" class="line" lang="plaintext"># name start alnSize strand seqSize alignment</span>
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<td class="new_line diff-line-num new" data-linenumber="4822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4822
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<pre style="margin: 0;">+<span id="LC4822" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="4823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4823
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<pre style="margin: 0;">+<span id="LC4823" class="line" lang="plaintext"># batch 0</span>
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4824
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<pre style="margin: 0;">+<span id="LC4824" class="line" lang="plaintext">a score=92 EG2=1e+09 E=8e-07 fullScore=102</span>
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<pre style="margin: 0;">+<span id="LC4825" class="line" lang="plaintext">s NW_017707804.1 0 70 + 70 AACACCACAATGAGATACCACCTCACAGCAGTCAGAATGGCTACAATTAACAAGTCAGGAAAGGACAGAT</span>
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<pre style="margin: 0;">+<span id="LC4826" class="line" lang="plaintext">s 57:130722274 0 54 + 54 AAAACCACAATGAGA---------------GTCAGAGTGGTGATTATTAA-AAGTCGAGAAATGATAGAT</span>
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<pre style="margin: 0;">+<span id="LC4827" class="line" lang="plaintext">p $&'~~~~~~~~~~~~(.0233.,,,,,+--&)*+,,,-.-+++++---)'%(+253--/111/0/,,+(%</span>
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<pre style="margin: 0;">+<span id="LC4828" class="line" lang="plaintext">c 20.6 0.00414 1.97 1.05 1.13 4.98 0.158 2.83 0.966 0.0011 9.56 0.997 0.0153 0.0037 1.07 6.54 51.8 16.4 0.361 3 0.27</span>
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<pre style="margin: 0;">+<span id="LC4829" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4830" class="line" lang="plaintext"># Query sequences=1</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#fcd3167fe23623673ee838f0da31855d3d479dff"><strong>test/last-test.sh</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">@@ -236,6 +236,10 @@ trap 'rm -f $db*' EXIT</td>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="shell"> lastdb <span class="nt" style="color: #000080;">-uRY8-8</span> <span class="nt" style="color: #000080;">-B1</span> <span class="nv" style="color: #008080;">$db</span> hg19-M.fa</span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="shell"> lastdb <span class="nt" style="color: #000080;">-uRY8</span> <span class="nt" style="color: #000080;">-B1</span> <span class="nv" style="color: #008080;">$db</span> hg19-M.fa</span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="shell"> lastal <span class="nt" style="color: #000080;">-fTAB</span> <span class="nt" style="color: #000080;">-q8</span> <span class="nt" style="color: #000080;">-b4</span> <span class="nv" style="color: #008080;">$db</span> galGal3-M-32.fa</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># tricky Forward-Backward bug that happened once</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="shell"> lastdb <span class="nv" style="color: #008080;">$db</span> alli.fa</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="shell"> lastal <span class="nt" style="color: #000080;">-j7</span> <span class="nt" style="color: #000080;">-r5</span> <span class="nt" style="color: #000080;">-q5</span> <span class="nt" style="color: #000080;">-a15</span> <span class="nt" style="color: #000080;">-b3</span> <span class="nv" style="color: #008080;">$db</span> huma.fa</span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> 2>&1 |</span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> version | diff <span class="nt" style="color: #000080;">-u</span> last-test.out -</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/cf76fa7e236ed8adc40b6c2c1f9011646941aebd#3aad58d94722f885e09fe11af2ffb43e844e3ba2"><strong>test/split1.maf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># a=31 b=1 A=21 B=3 e=190 d=94 x=189 y=48 z=189 D=1e+09 E=0.516058</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># R=01 u=0 s=2 S=1 M=0 T=0 m=100 l=1 n=100 k=1 w=1000 t=4.75495 j=3 Q=0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># /home/mcfrith/data/genome/calMil1/last/calMil1-uMAM8</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># Reference sequences=21204 normal letters=936953443</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># lambda=0.214243 K=0.246122</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># A C G T M S K W R Y B D H V</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># A 5 -7 -3 -6 2 -5 -4 2 3 -6 -5 1 1 1</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># C -8 5 -7 -2 2 2 -4 -4 -7 3 1 -5 1 0</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># G -2 -7 5 -8 -4 2 2 -4 3 -7 0 1 -5 1</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># T -6 -3 -7 5 -4 -5 2 2 -6 3 1 1 1 -5</span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># M 2 2 -5 -4 2 0 -4 0 0 0 -1 -1 1 1</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># S -4 2 2 -4 0 2 0 -4 0 0 1 -1 -1 1</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># K -4 -5 2 2 -4 0 2 0 0 0 1 1 -1 -1</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># W 2 -5 -5 2 0 -5 0 2 0 0 -1 1 1 -1</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># R 3 -7 3 -7 0 0 0 0 3 -7 -2 1 -1 1</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># Y -7 3 -7 3 0 0 0 0 -7 3 1 -1 1 -2</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># B -5 1 1 1 -1 1 1 -1 -1 1 1 0 0 0</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># D 1 -5 1 0 -1 -1 1 1 1 -2 -1 1 -1 0</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># H 0 1 -5 1 1 -1 -1 1 -2 1 0 -1 1 -1</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># V 1 1 1 -5 1 1 -1 -1 1 -1 0 0 0 1</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># Coordinates are 0-based. For - strand matches, coordinates</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># in the reverse complement of the 2nd sequence are used.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">#</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"># name start alnSize strand seqSize alignment</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">#</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"># m=1 s=190</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">#</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"># Query sequences=195</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">a score=211 mismap=0.00255</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">s KI635889 4462115 58 + 6429418 TACCTATAGATTGGTTGACAGCTTTCATGCACAAATTTTCCACCAGAATCTTTCCTGG</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">s chr1 248943367 58 - 248956422 TGCCTATGGACTGGTTGACAGCCTTCATGCACAGGTTCTCCACCAGAGCCTTTCTTGG</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">p #$)-1356899::::::::::::::::::::::::::::::::::::9888640,+(%</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">a score=331 mismap=1e-10</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">s KI635917 1140607 159 + 4339253 ACCTTGTTcttgttccttctgcttcttcttcttctccatcttaatcAGCTTTGCATTGCGCAGTTTGGCCTTTCCAATGCCTCCGGCCTGACGAATGGATTCCAGCAGACTAGCCCTTCCATCCGAGGGTTTCACAACCTCCTTGGGTGCCCCCTGGAC</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">s chr1 15793 155 + 248956422 ACCTTGCTCctgctccttctgctgctg---cttctccaGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGG-CCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGAC</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">p %*.2578<>?BDFJMOPPQQQQQQQQQQQQUY\^___________```bbccccdejnsw{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{zwtpkgbb``^^^^^^^^^^^^^^^^]]\\\\[[[[ZZXUTROKGFDBA>;73.*%</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">a score=520 mismap=1e-10</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">s KI635917 1143406 188 + 4339253 TCTGTGCTGAACGTGGGCAGTTCAGGCATGTTGCTTCCTGGCACGGAGGGCGCGATGCCAGGTCCCAGGTCAGCACTGTACATGAGGTCATCTGCAATCCCAGGCAGATCCGGTAGGTAGGATGGGACGTCAATCTCTGGGACCTGACCCAGGTCTGGTACATAGAAGTAATTCTCAGTAGTCTGAAA</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">s chr1 16876 185 + 248956422 TCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGC---CAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAA</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">p #$%()**+.1237<@EILOPQQQQQQQQQQQQQQQQQRRSTTUXY]begiimoquz}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}xsojigc_[VRMID?;:740+'&$$$$$$#"""</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">a score=340 mismap=1e-10</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">s KI635917 1144102 140 + 4339253 ACCCGTCTTTCTAGTTGCTCTCGCGTGGTGATTGAGAGCGGGGCATCAAACGGCTTCTCTTCCTTCTCAGTCTCCAGTGCCATGTGTGTCTTTGTCACAGCTCCTGCTAACGGATCCAAGAGAACGTACTTCTTGTAGCT</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">s chr1 17230 140 + 248956422 ACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCT</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">p #%%&&&''+.12589=BEHJKLLLMOPQTWXYYZZ[\\\afjosx|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|xsonljihfecbbba`_]ZVURONMLIHFC?;62-((&$$#</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">a score=334 mismap=1e-10</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">s KI635917 1144725 145 + 4339253 TACGGATTCTCAGTAGTGTTGAACAGCAGCAGGGAGCTGATGGAGCTAATGTTCCGAGGAAGGCTTCCCAACCCCTCCTCCGTCTCATCCTCCTCTCGAGACTTGGTGTTCAGACACACGGGGTAATGCTTTGCCTTTTCCTGAG</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">s chr1 17602 145 + 248956422 TACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">p $(*+-/37;?ABEHINRW[_cegglpuy}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}yxvuttssrplhdcccccccccccccccba`^[ZZZXVRNLJFEEDCBBBA>>===<::862.*%</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">a score=340 mismap=1e-10</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">s KI635917 1146887 159 + 4339253 CACACCTGCACAGCCTTATCATCCAGAGGCTTCAGCTTGCTGTGGATCTTGTAGCGTGGGCGCTTCTGAGAAGCAGGATCATCCGCGCCCGAGAATATGGAAGTGTAATCCTGTAGCCGGTCAGGTGCAGGGTACTTAGCACTGGAAAAGACCTGCAGA</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">s chr1 17909 159 + 248956422 CAGACCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTGTGGA</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">p #$%).1456667888889;=>@AAAAAAAAAAABGKPTWZ[\`eimqstx{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~zvrmhd_^\XTPKGB><:6652/+'%$#</span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">a score=240 mismap=7.38e-06</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">s KI635917 1147176 117 + 4339253 TACTTTTGTGGCTTTCTTGCTGCCTTTGATCCTCTCGATCTTGGCCTGTGCCAGATTGATGCGGTCACTGATGGACTGCAGGCGAGTCTGATTCCTCTCCACGTTTTGGGAAACCCT</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">s chr1 18264 117 + 248956422 TACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCT</span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">p $'()*++-159;=AEJNQRSTTTTTTTTTTTTTTTTTTTTTTTTTTSSQQPOLHGGFFFFFFFFFFFFFFFFFFFFEEECA@@@@@@@@@@??????>>=<;987777642.-+*($</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">a score=252 mismap=4.27e-07</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">s KI635917 1161884 119 + 4339253 ACCTCGTGAAGACATCATTGGAGATTTTTTGGAGATACTGAAGAGCATCAGTGATCTGGTGAATGGACTCTTCCCGGCGCAGGTCCGGCTGGATTATTGGCACCGTGTACACCTGTCCT</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">s chr1 24735 119 + 248956422 ACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCT</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">p #%&&''+/35667778889:>ACDEFIKLNOOSUVZ]^___``````````````````````````````````````````_]ZYWSOKFB=987666542/.-,,+*))))('&%#</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">a score=192 mismap=0.109</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">s KI635862 2418195 96 + 12728579 CACAGGCCGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCCGA-GCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">s chr1 248924753 98 - 248956422 CATAGCTCACTGCAGCCTCGATCTCCCAAGCTCAAGTGATCCTCCCGCCTCAGCCTCCCATGTAGCTGGGACTACAGGTGTGTGACACCATGACTGGC</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">p #$%%&&'(()*****************************************************************************))(''&&%%$#</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">a score=201 mismap=0.031</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">s KI635862 2418214 77 + 12728579 GAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC--GAGCAGCCGGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">s chr1 248920976 79 - 248956422 GAACTCCTGGCCTCAAGCGATCCTCCCACCTCAGCCTCCCAAAGTGTTGGGATTATAGACATGAGCCACTGCACCTGGC</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">p %),.//00000000000000000000000000000000000000000000000000000000000///////..-*)($</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">a score=214 mismap=0.00137</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">s KI635862 2418214 80 + 12728579 GAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC--GAGCAGCCGGATAACAGGCGCGCGCCACCGCGCCCGGCGAG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">s chr1 248916719 82 - 248956422 GAACTCCTGACCTCAGGTGATCCACCCGCCTCAGCCTCCCAAAGTGTTGGGATTACAGGCACGAGCCACTGCATCCAGCCAG</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">p %*.269;<==========================================================<<:87410/.+*($$#</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">a score=214 mismap=0.00209</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">s KI635862 2418214 77 + 12728579 GAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCCGAGCAGCC--GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">s chr1 248879450 79 - 248956422 GAATTCCTGGCCTCAAGTGATCTGCCCGCCTCAGCCTCCCAAAATGCTGGGATCACAGGCATGAGCCACCACGCCCGGC</span>
</pre>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">p %(+,158:;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;::862.*%</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">a score=198 mismap=0.0234</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">s KI635862 2418209 85 + 12728579 GCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC--GAGCAGCCGGATAACAGGCGCGCGCCACCGCGCCCGGCGAG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">s chr1 248845257 87 - 248956422 GTCCCGAACTCCTGACCTTAGGTGATCCACCAGCATCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGTCCAGCCAG</span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">p #$&'(+.001111111111111111111111111111111111111111111111111111111111111111100//..-*)'$$#</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">a score=190 mismap=0.228</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">s KI635862 2418217 74 + 12728579 CTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCCG-AGCAGCCGG-ATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">s chr1 248845129 76 - 248956422 CTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGTATTACAGGTGCCTGCCACCACACCCAGC</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">p $%&''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''&&%$#</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">a score=194 mismap=0.127</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">s KI635862 2418218 73 + 12728579 TCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">s chr1 248826215 75 - 248956422 TCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTGTGCCACCACACCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">p $'()))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))('$</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">a score=192 mismap=0.12</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">s KI635862 2418202 89 + 12728579 CGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">s chr1 248811964 91 - 248956422 CACTGCAGCCTCCACCTGCCAGGCTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTAAGTGCCACCACACCCAGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">p #$'())))))))))))))*****************************************************************))))(&%#</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">a score=191 mismap=0.124</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">s KI635862 2418206 85 + 12728579 GCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">s chr1 248811595 87 - 248956422 GCAACCTCCACCTTCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGTTGGGATTACAGGCATGTGCCACCATGCCCAGC</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">p "##$$$$$$%%'(())))))*********************************************************))))))(&%#</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">a score=207 mismap=0.00555</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">s KI635862 2418202 89 + 12728579 CGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">s chr1 248806800 91 - 248956422 CACTGCAACCTTCACCTTCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGCCCGCCACCATACCCAGC</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">p #%(,.///000001145567777777777777777777777777777777777777777777777777777777777776530/..-+(&$</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">a score=192 mismap=0.117</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">s KI635862 2418195 96 + 12728579 CACAGGCCGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTC-CGAGCAGCCGG-ATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">s chr1 248803921 98 - 248956422 CATAGCTCACTGCAGCCTTGACCTCCTAGGCTAAAGCAATCCTCCCACCTTAGCCTCTCCAGTAGCTGGAACTACAGGCATGCATCACCATGTCCAGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">p #$$%&&'(()*******************************************************************************)))(('&%#</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">a score=330 mismap=0.75</span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">s KI636063 409336 105 + 789923 AAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCCATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAGCGAGCA</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">s chr1 157784 102 + 248956422 aaaataTGGAATGCTTCACAAATTTGCATGTCATTCTTTCACAGAGGCCGTGCCAA---TCTCTCTATTGTTCCAACTTAAGTATGTGTGCTACTGAGGCAAGCA</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">p !"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""!</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">a score=203 mismap=0.0127</span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">s KI635862 2418202 85 + 12728579 CGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTC-CGAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCC</span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">s chr1 248798099 87 - 248956422 CACTGCAGCCTCAACCTCCTGGGCTCAAGCAATCCTCCTGCCTCAGCCTCACAAGTAGCTGGGACTACAGGTGCTTGTCACCACACC</span>
</pre>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">p #%)-01233333333333333333333333333333333333333333333333333333333333333333322211110.*)'&$</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">a score=201 mismap=0.0167</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">s KI635862 2418211 79 + 12728579 CCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC--GAGCAGCCGGATAACAGGCGCGCGCCACCGCGCCCGG</span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">s chr1 248796986 81 - 248956422 CTAGAACTTTTGACCTCAGGTGATCCGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGATCCACCGCGCCCAG</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">p #%),/11222222222222222222222222222222222222222222222222222222222222222222221/-)%#</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">a score=209 mismap=0.00211</span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">s KI635862 2418209 87 + 12728579 GCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC--GAGCAGCCGGATAACAGGCGCGCGCCACCGCGCCCGGCGAGGG</span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">s chr1 248792490 89 - 248956422 GTCTAGAACTCCTGACCTTGGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCTGGG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">p #$'(-158:;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;:9740,+($$$#"</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">a score=271 mismap=6.21e-09</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">s KI635901 1311390 127 + 5048387 TCTTTTTTTCCTTCTGTCAACACTTTTAGCTGAAGCCATAAAAACGACAAGTCCCGTCATAATCCCATACCCACTCTTTCAGTCCAATGCTGAAGATCTTAGTGTTGAAGGTTTACCCGAAGGTATT</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">s chr1 248791606 123 - 248956422 TCCCTttttctttttttt----CTTATAGCTCGAGCTGTAAAAGCCAAAGGTCCGGTGATGATCCCATACCCTTTTTTCCAGTCTCATGTTGAAGATTTTTATGTAGAAGGCCTtcccaaaggaatt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">p "##$&'''''''''''''''''+./048:;<<=ACEFGKNQRSSSSTTWX\_abbdefikloqrrrssssssssssssssssssrrrrrrrrqolid`^\XXWVTQQOMIEA@?>>=;8752.)('$</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">a score=202 mismap=0.0217</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">s KI635862 2418204 87 + 12728579 CTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">s chr1 248790144 89 - 248956422 CTGCAACCTCCACCTCCTGGGTTCAGGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGCCTGCCACCATGCCCAGC</span>
</pre>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">p $')*+++++++,-/011111111111111111111111111111111111111111111111111111111111111111000/.+(&$</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">a score=191 mismap=0.145</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">s KI635862 2418202 87 + 12728579 CGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCT-CCGAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCCCG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">s chr1 167211 89 + 248956422 CACTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTCCTGCCTTGGCCTCCCGAATAGCTGGGATTACAGACATGCGCCACCACACCCG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">p "#%&&&'''''''''()))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))((('&$</span>
</pre>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">a score=192 mismap=0.162</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">s KI635862 2418214 77 + 12728579 GAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC--GAGCAGCCGGATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">s chr1 248786969 79 - 248956422 GAACTCCTGACCTCAAGTGATCCACCCATCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGAGCCCAGC</span>
</pre>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">p $&((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((('&%#</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">a score=194 mismap=0.0422</span>
</pre>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">s KI635862 2418197 97 + 12728579 CAGGCCGCTGCAGCC-CAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCCG-GATAACAGGCGCGCGCCACCGCGCCCGGCGAG</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">s chr1 248786816 100 - 248956422 CAGTTCACTGCAACCTCTGCCCCCCTGGGTTCAAACAATTCTCCTGTCTCAGCCTCCTGAGTAGCTGAGATTACAGGCATGTGCCACCATGCCCGGCTAG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">p "###$%%&&&''''''''''')*,-.....................................................................-+($$#</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">a score=199 mismap=0.0162</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">s KI635862 2418217 87 + 12728579 CTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCCGG-ATAACAGGCGCGCGCCACCGCGCCCGGCGAGGGTTGCGGCT</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">s chr1 248781694 89 - 248956422 CTTTTGGGTTCAAGGGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGTGCCACCACACCCGGCTAATGTTGTAGTT</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">p #$%&)*++,/12222222222222222222222222222222222222222222222222222222222222221/-,+++**(&%$#"</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">a score=226 mismap=0.000106</span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">s KI635862 2418202 89 + 12728579 CGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCCGG-ATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">s chr1 248781029 91 - 248956422 CACTGCAACCTCCACCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGGCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCATGCCCAGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">p #%),./0000000226:<>>@@ABEGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGFC@;75530,('$</span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">a score=194 mismap=0.0709</span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">s KI635862 2418197 94 + 12728579 CAGGCCGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTCC-GAGCAGCCGG-ATAACAGGCGCGCGCCACCGCGCCCGGC</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">s chr1 175660 96 + 248956422 CAGCTCACTGCAATCTCTGCCCCCTGGGTTCAAGCAATTCTCCTTCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCATGCACCACCACGCCTGGC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">p "###$%%&''''''''''''))++,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,+))'$</span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">a score=211 mismap=0.00255</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">s KI635889 4462115 58 + 6429418 TACCTATAGATTGGTTGACAGCTTTCATGCACAAATTTTCCACCAGAATCTTTCCTGG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">s chr1 248772848 58 - 248956422 TGCCTATGGACTGGTTGACAGCCTTCATGCACAGGTTCTCCACCAGAGCCTTTCTTGG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">p #$)-1356899::::::::::::::::::::::::::::::::::::9888640,+(%</span>
</pre>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">a score=392 mismap=1e-10</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">s KI635917 1140607 159 + 4339253 ACCTTGTTcttgttccttctgcttcttcttcttctccatcttaatcAGCTTTGCATTGCGCAGTTTGGCCTTTCCAATGCCTCCGGCCTGACGAATGGATTCCAGCAGACTAGCCCTTCCATCCGAGGGTTTCACAACCTCCTTGGGTGCCCCCTGGAC</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">s chr1 186314 156 + 248956422 ACCTTGCTCctgctccttctg---cttcttcttctccAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTCGACCACTTCCCTGGGAGCTCCCTGGAC</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">p %*.2578;>?BDEHJKKKKKKKKKPUY^bgkortuuuuuuuuuuuuvvwxxyyyz{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~zvvuutsrpponkgcbaa``___^]\YVUROKGFDBA>;73.*%</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">a score=513 mismap=1e-10</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">s KI635917 1143406 188 + 4339253 TCTGTGCTGAACGTGGGCAGTTCAGGCATGTTGCTTCCTGGCACGGAGGGCGCGATGCCAGGTCCCAGGTCAGCACTGTACATGAGGTCATCTGCAATCCCAGGCAGATCCGGTAGGTAGGATGGGACGTCAATCTCTGGGACCTGACCCAGGTCTGGTACATAGAAGTAATTCTCAGTAGTCTGAAA</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">s chr1 187398 185 + 248956422 TCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGC---CAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGACAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAA</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">p #$%()**+.1237<@EILOPQQQQQQQQQQQQQQQQQRRSTTUXY]begiimoquz}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}xsojigc_[VRMID?;:740+'&$$$$$$#"""</span>
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201
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