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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Nilesh Patra pushed to branch master at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kma/-/commit/79d1c6be10a06c8ac2a069a8d31177261024f9fb">79d1c6be</a></strong>
<div>
<span> by Nilesh Patra </span> <i> at 2023-01-29T15:05:19+05:30 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 1.4.11</pre>
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<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kma/-/commit/b3bad021a950db38318f4d075ab7977aa921133d">b3bad021</a></strong>
<div>
<span> by Nilesh Patra </span> <i> at 2023-01-29T15:05:20+05:30 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/1.4.11'
Update to upstream version '1.4.11'
with Debian dir e2245c7d42d0cd4fa515e2bf53246e76d553e1f3</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/kma/-/commit/836d384bb7410ed9a4e3439bf4a198e891378972">836d384b</a></strong>
<div>
<span> by Nilesh Patra </span> <i> at 2023-01-29T15:05:40+05:30 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Upload to unstable
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
5 changed files:
</h4>
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<li class="file-stats">
<a href="#302e1fff50e6c455134afebd2f2fa2f0c5b717d8">
alnfrags.c
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#e2f107808c49d5d6f77fb3068e9888f395db3c99">
updatescores.c
</a>
</li>
<li class="file-stats">
<a href="#f611e64d8da9b4c9e7c46f8c02da8ed8d0efef62">
updatescores.h
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="302e1fff50e6c455134afebd2f2fa2f0c5b717d8">
<a href="https://salsa.debian.org/med-team/kma/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972#302e1fff50e6c455134afebd2f2fa2f0c5b717d8"><strong style="font-weight: bold;">alnfrags.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1077,7 +1077,6 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa</td>
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<td class="old_line diff-line-num" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1077
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<td class="new_line diff-line-num" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1077
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1077" class="line" lang="c"> <span class="n" style="color: #333;">Wl</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">NWmatrices</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1078
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<td class="new_line diff-line-num" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1078
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1078" class="line" lang="c"> <span class="n" style="color: #333;">arc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1079
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<td class="new_line diff-line-num" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1079
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1079" class="line" lang="c"> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1080
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<td class="new_line diff-line-num old" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1080" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1081
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<td class="new_line diff-line-num" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1080
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1080" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">t_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;">t_i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">matched_templates</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t_i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1082
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<td class="new_line diff-line-num" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1081
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1081" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1083
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<td class="new_line diff-line-num" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1082
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1082" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check if index DB is loaded */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1207,8 +1206,8 @@ int alnFragsSE(HashMapCCI **templates_index, int *matched_templates, int *templa</td>
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<td class="old_line diff-line-num" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1207
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<td class="new_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1206
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1206" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1208
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<td class="new_line diff-line-num" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1207
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1207" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1209
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<td class="new_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1208
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1208" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1210
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<td class="new_line diff-line-num old" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1210" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//update_Scores(qseq, q_len, minFrac, bestHits, *best_read_score, bestLen, best_start_pos, best_end_pos, bestTemplates, Scores, Lengths, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1211
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<td class="new_line diff-line-num old" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1211" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Lengths</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1209" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right addition" style="background-color: #c7f0d2;">*matched_templates = </span>update_Scores(qseq, q_len, minFrac, bestHits, *best_read_score, bestLen, best_start_pos, best_end_pos, bestTemplates, Scores, Lengths, header, *flag, alignment_scores, uniq_alignment_scores, frag_out_raw);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1210" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Lengths</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1212
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<td class="new_line diff-line-num" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1211
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1211" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1213
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<td class="new_line diff-line-num" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1212
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1212" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1214
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<td class="new_line diff-line-num" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1213
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1213" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1432,7 +1431,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<td class="old_line diff-line-num" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1432
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<td class="new_line diff-line-num" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1431
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1431" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1433
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<td class="new_line diff-line-num" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1432
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1432" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1434
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<td class="new_line diff-line-num" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1433
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1433" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1435
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<td class="new_line diff-line-num old" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1435" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1434" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1436
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<td class="new_line diff-line-num" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1435
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1435" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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1437
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1436
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1436" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1437
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1437" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">rc</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="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1442,7 +1441,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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1442
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<td class="new_line diff-line-num" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1441
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1441" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1443
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1442
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1442" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1444
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<td class="new_line diff-line-num" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1443
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1443" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1445
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<td class="new_line diff-line-num old" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1445" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1444
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1444" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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1446
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<td class="new_line diff-line-num" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1445" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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1447
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1447" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1511,8 +1510,8 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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1511
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<td class="new_line diff-line-num" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1510
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1510" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestLen,</span></span>
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1512
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<td class="new_line diff-line-num" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1511
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1511" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Lengths</span></span>
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1513
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1512
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1512" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="new_line diff-line-num old" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1514" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1515
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<td class="new_line diff-line-num old" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1515" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1513
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1513" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1514
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1514" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">+=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1516
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<td class="new_line diff-line-num" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1515
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1515" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1517
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<td class="new_line diff-line-num" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1516
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1516" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1518
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<td class="new_line diff-line-num" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1517
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1517" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1547,7 +1546,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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1547
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<td class="new_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1546
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1546" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1548
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<td class="new_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1547
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1547" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1549
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<td class="new_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1548
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1548" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1550
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<td class="new_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1550" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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1549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1549" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1551
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<td class="new_line diff-line-num" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1550
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1550" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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1552
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1551
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1551" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1553
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<td class="new_line diff-line-num" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1552
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1552" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1584,7 +1583,7 @@ int alnFragsUnionPE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<td class="old_line diff-line-num" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1584
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<td class="new_line diff-line-num" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1583
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1583" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestLen,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1585
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<td class="new_line diff-line-num" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1584
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1584" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Lengths</span></span>
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<td class="old_line diff-line-num" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1586
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<td class="new_line diff-line-num" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1585
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1585" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1587
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<td class="new_line diff-line-num old" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1587" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1586
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1586" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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1588
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<td class="new_line diff-line-num" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1587
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1587" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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1589
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1588
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1588" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1590
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<td class="new_line diff-line-num" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1589
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1589" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1809,7 +1808,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<td class="old_line diff-line-num" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1809
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<td class="new_line diff-line-num" data-linenumber="1808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1808
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1808" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1810
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<td class="new_line diff-line-num" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1809
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1809" class="line" lang="c"> <span class="p">}</span></span>
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1811
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<td class="new_line diff-line-num" data-linenumber="1810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1810
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1810" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1812
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<td class="new_line diff-line-num old" data-linenumber="1811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1812" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1811
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1811" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1813
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<td class="new_line diff-line-num" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1812
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1812" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1814
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<td class="new_line diff-line-num" data-linenumber="1813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1813
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1813" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1815
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<td class="new_line diff-line-num" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1814
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1814" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">rc</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="1819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1819,7 +1818,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<td class="old_line diff-line-num" data-linenumber="1819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1819
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<td class="new_line diff-line-num" data-linenumber="1818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1818
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1818" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1820
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<td class="new_line diff-line-num" data-linenumber="1819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1819
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1819" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1821
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<td class="new_line diff-line-num" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1820
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1820" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1822
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<td class="new_line diff-line-num old" data-linenumber="1821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1822" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1821
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1821" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1823
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<td class="new_line diff-line-num" data-linenumber="1822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1822
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1822" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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1824
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1823
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1823" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1825
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<td class="new_line diff-line-num" data-linenumber="1824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1824
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1824" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1889,8 +1888,8 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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1889
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<td class="new_line diff-line-num" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1888
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1888" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestLen,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1890
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<td class="new_line diff-line-num" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1889
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1889" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Lengths</span></span>
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<td class="old_line diff-line-num" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1891
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<td class="new_line diff-line-num" data-linenumber="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1890
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1890" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1892
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<td class="new_line diff-line-num old" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1892" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1893
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<td class="new_line diff-line-num old" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1893" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1891
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1891" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1892
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1892" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">+=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">matched_templates</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1894
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<td class="new_line diff-line-num" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1893
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1893" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1895
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<td class="new_line diff-line-num" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1894
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1894" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1896
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<td class="new_line diff-line-num" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1895
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1895" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1925,7 +1924,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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1925
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<td class="new_line diff-line-num" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1924
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1924" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1926
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<td class="new_line diff-line-num" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1925
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1925" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1927
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<td class="new_line diff-line-num" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1926
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1926" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1928
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<td class="new_line diff-line-num old" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1928" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1927
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1927" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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1929
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<td class="new_line diff-line-num" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1928
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1928" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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1930
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1929
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1929" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1931
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<td class="new_line diff-line-num" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1930
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1930" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -1962,7 +1961,7 @@ int alnFragsPenaltyPE(HashMapCCI **templates_index, int *matched_templates, int</td>
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<td class="old_line diff-line-num" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1962
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<td class="new_line diff-line-num" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1961
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1961" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> bestLen,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1963
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<td class="new_line diff-line-num" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1962
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1962" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Lengths</span></span>
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<td class="old_line diff-line-num" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1964
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<td class="new_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1963
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1963" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1965
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<td class="new_line diff-line-num old" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC1965" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1964
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1964" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_se</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score_r</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1966
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<td class="new_line diff-line-num" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1965
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1965" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1967
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<td class="new_line diff-line-num" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1966
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1966" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1968
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<td class="new_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
1967
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC1967" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2122,7 +2121,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<td class="old_line diff-line-num" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2122
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<td class="new_line diff-line-num" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2121
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2121" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">[</span><span class="n" style="color: #333;">t_i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2123
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<td class="new_line diff-line-num" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2122
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2122" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2124
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<td class="new_line diff-line-num" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2123
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2123" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2125
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<td class="new_line diff-line-num old" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2125" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="2126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2124" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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2126
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<td class="new_line diff-line-num" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2125
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2125" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2127
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<td class="new_line diff-line-num" data-linenumber="2126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2126" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2128
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<td class="new_line diff-line-num" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2127
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2127" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get rc flag */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -2139,7 +2138,7 @@ int alnFragsForcePE(HashMapCCI **templates_index, int *matched_templates, int *t</td>
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<td class="old_line diff-line-num" data-linenumber="2139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2139
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<td class="new_line diff-line-num" data-linenumber="2138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2138
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2138" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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2140
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2139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2139" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2141
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<td class="new_line diff-line-num" data-linenumber="2140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2140
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2140" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2142
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<td class="new_line diff-line-num old" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC2142" class="line" lang="c"> <span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2141" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">*</span></span><span class="n" style="color: #333;"><span class="idiff addition" style="background-color: #c7f0d2;">matched_templates</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333;">update_Scores_pe</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r_comp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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2143
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<td class="new_line diff-line-num" data-linenumber="2142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
2142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2142" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">excludeOut</span><span class="p">);</span></span>
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2144
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2143
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2143" class="line" lang="c"> <span class="p">}</span></span>
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2145
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2144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC2144" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: bold;">debian/changelog</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC1" class="line" lang="plaintext">kma (1.4.11-1) unstable; urgency=medium</span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC4" class="line" lang="plaintext"> * New upstream version 1.4.11</span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sun, 29 Jan 2023 15:05:28 +0530</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC7" class="line" lang="plaintext"></span>
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1
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC8" class="line" lang="plaintext">kma (1.4.10-1) unstable; urgency=medium</span>
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2
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<a href="https://salsa.debian.org/med-team/kma/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972#e2f107808c49d5d6f77fb3068e9888f395db3c99"><strong style="font-weight: bold;">updatescores.c</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -200,7 +200,7 @@ void update_Scores_nanoold(unsigned char *qseq, int q_len, double minFrac, int c</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC201" class="line" lang="c"><span class="p">}</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC202" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC203" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestReadScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Lengths</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC203" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestReadScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Lengths</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC204" class="line" lang="c"> </span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC205" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC206" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestStart</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestEnd</span><span class="p">;</span></span>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -251,8 +251,8 @@ void update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter,</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC251" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC252" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC253" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
254
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<td class="new_line diff-line-num old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">-</span></span><span class="n" style="color: #333;">minFrac</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
255
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<td class="new_line diff-line-num old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">minFrac</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">-</span></span><span class="n" style="color: #333;">minFrac</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bestReadScore</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minFrac</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">minFrac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minFrac</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bestReadScore</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
256
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<td class="new_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC256" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
257
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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
257
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Scores</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
258
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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
258
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC258" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">Lengths</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">minScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">minFrac</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -293,9 +293,11 @@ void update_Scores(unsigned char *qseq, int q_len, double minFrac, int counter,</td>
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<td class="old_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
293
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<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestStart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
294
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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestEnd</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
295
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC296" class="line" lang="c"> </span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC297" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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296
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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC298" class="line" lang="c"><span class="p">}</span></span>
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297
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299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC299" class="line" lang="c"></span>
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298
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<td class="new_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC298" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_se</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC300" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_se</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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299
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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: inherit;" align="right" bgcolor="#fafafa">
301
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC301" class="line" lang="c"> </span>
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300
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<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
302
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC302" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</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: inherit;" align="right" bgcolor="#fafafa">
301
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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: inherit;" align="right" bgcolor="#fafafa">
303
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC303" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestStart</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestEnd</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -381,9 +383,11 @@ void update_Scores_se(unsigned char *qseq, int q_len, double minFrac, int counte</td>
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<td class="old_line diff-line-num" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
381
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<td class="new_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
383
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC383" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestStart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
382
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<td class="new_line diff-line-num" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
384
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestEnd</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
383
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<td class="new_line diff-line-num" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
385
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC385" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC386" class="line" lang="c"> </span>
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<td class="old_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC387" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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384
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<td class="new_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
388
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC388" class="line" lang="c"><span class="p">}</span></span>
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385
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<td class="new_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
389
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC389" class="line" lang="c"></span>
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386
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<td class="new_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC386" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_pe</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC390" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_pe</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
387
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<td class="new_line diff-line-num" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
391
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC391" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
388
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<td class="new_line diff-line-num" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
392
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC392" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" 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: inherit;" align="right" bgcolor="#fafafa">
389
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<td class="new_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
393
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC393" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestStart</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestEnd</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -479,6 +483,8 @@ void update_Scores_pe(unsigned char *qseq, int q_len, unsigned char *qseq_r, int</td>
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<td class="old_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
479
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<td class="new_line diff-line-num" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
483
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC483" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">),</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
480
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<td class="new_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
484
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC484" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
481
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<td class="new_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
485
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC485" class="line" lang="c"> <span class="n" style="color: #333;">sfwrite</span><span class="p">(</span><span class="n" style="color: #333;">header_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
486
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC486" class="line" lang="c"> </span>
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<td class="old_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
487
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC487" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
482
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<td class="new_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
488
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC488" class="line" lang="c"><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
483
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<td class="new_line diff-line-num" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
489
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC489" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
484
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<td class="new_line diff-line-num" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
490
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC490" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_old</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972#f611e64d8da9b4c9e7c46f8c02da8ed8d0efef62"><strong style="font-weight: bold;">updatescores.h</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -22,8 +22,8 @@</td>
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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC22" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC23" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_pe_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestReadScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Lengths</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_se</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">void</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_pe</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestReadScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Lengths</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_se</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">int</span></span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_pe</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minFrac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
28
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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
28
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_old</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">update_Scores_pe_old</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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;">qseq_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qr_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frag_out_raw</span><span class="p">);</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/kma/-/compare/27b21a9a1cd4d0f026f752a3ae77cfeec4760e7b...836d384bb7410ed9a4e3439bf4a198e891378972#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong style="font-weight: bold;">version.h</strong></a>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC19" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.4.1<span class="idiff left right deletion" style="background-color: #fac5cd;">0</span>"</span></span></pre></td>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.4.1<span class="idiff left right addition" style="background-color: #c7f0d2;">1</span>"</span></span></pre></td>
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