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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pftools">Debian Med / pftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696">b51b2b73</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-23T14:12:57+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.8</pre>
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<h4>15 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#56cd058343dc500d70fb6c2c4aac98dc5da7cbe5">
<span class="new-file">
+
Docker/Dockerfile
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<li class="file-stats">
<a href="#59e70f737a878c10c711a056493a7d58029945cc">
<span class="new-file">
+
Docker/README.docker
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#43609a23d2d5dd48390d5916d1702758bb3590f5">
src/C/prg/pfscan.c
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<li class="file-stats">
<a href="#4733e34ee0817b24a38b0933ce77ea2d5dddcb57">
src/C/utils/io.c
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<li class="file-stats">
<a href="#7a731b6883e1e46023ef4242a666319467b1ab47">
src/C/utils/system.c
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<li class="file-stats">
<a href="#9582d93fae3e6b87bdd789bae160015c4e7e584b">
src/Perl/fasta_to_fastq.pl
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<li class="file-stats">
<a href="#ee04dec7a60199805f8be996699b7f1ddf7e4823">
src/Perl/make_iupac_cmp.pl
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<li class="file-stats">
<a href="#a90d30287a920b2225b061ac70a46ee73c5957b1">
src/Perl/scramble_fasta.pl
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<li class="file-stats">
<a href="#b007c65aa0694800395c0bf1394f95c3549e455c">
src/Perl/sort_fasta.pl
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<li class="file-stats">
<a href="#edc76d1689c1a7f0bd0401f05fd6b05ea7f6e15b">
tests/examples/test_V3.sh.cmake
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<li class="file-stats">
<a href="#25ebe0897656d14d609c490fa9e73f26e61ed9f0">
tests/examples/test_V3_output.sh.cmake
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<li class="file-stats">
<a href="#0130171c343ee37c2f9a892a3094cf0a7c3a3d01">
tests/examples/test_pfsearchV3_iupac.pl.cmake
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<li class="file-stats">
<a href="#e49e80e7fdd233ba13714866dbec311e937d3a73">
tests/examples/test_scan_search.pl.cmake
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#########################################################################################</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># PfTools versioning</span></span>
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3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>VERSION <span class="s2" style="color: #d14;">"3.2.<span class="idiff left right">6</span>"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>VERSION <span class="s2" style="color: #d14;">"3.2.<span class="idiff left right">8</span>"</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>MAJOR_VERSION <span class="s2" style="color: #d14;">"3"</span><span class="p">)</span></span>
</pre>
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6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>MINOR_VERSION <span class="s2" style="color: #d14;">"2"</span><span class="p">)</span></span>
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7
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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>PATCH_VERSION <span class="s2" style="color: #d14;">"<span class="idiff left right">6</span>"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>PATCH_VERSION <span class="s2" style="color: #d14;">"<span class="idiff left right">8</span>"</span><span class="p">)</span></span>
</pre>
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8
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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: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>DATA_PATH <span class="s2" style="color: #d14;">"share/data"</span> CACHE STRING <span class="s2" style="color: #d14;">"Installation data folder"</span> <span class="p">)</span></span>
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9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>DOC_PATH <span class="s2" style="color: #d14;">"share/doc"</span> CACHE STRING <span class="s2" style="color: #d14;">"Installation doc folder"</span> <span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>MAN1_PATH <span class="s2" style="color: #d14;">"share/man/man1"</span> CACHE STRING <span class="s2" style="color: #d14;">"Installation man1 folder"</span> <span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -396,7 +396,7 @@ ADD_SUBDIRECTORY(data)</td>
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<td class="old_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
396
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<td class="new_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#########################################################################################</span></span>
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<td class="old_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
397
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<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Enabling TESTING</span></span>
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398
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CTest<span class="p">)</span></span>
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399
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<td class="new_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>TESTS_DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_<span class="idiff left right">BINARY</span>_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/Tests"</span> CACHE PATH <span class="s2" style="color: #d14;">"Directory for tests"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>TESTS_DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_<span class="idiff left right">SOURCE</span>_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/Tests"</span> CACHE PATH <span class="s2" style="color: #d14;">"Directory for tests"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>TESTS_DATA_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/tests"</span><span class="p">)</span></span>
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401
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>NOT EXISTS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">TESTS_DIRECTORY</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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402
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FILE</span><span class="p">(</span>MAKE_DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">TESTS_DIRECTORY</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#56cd058343dc500d70fb6c2c4aac98dc5da7cbe5"><strong>Docker/Dockerfile</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:20.04 AS compile</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> PFTOOLS_VERSION</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> BUILD_DATE</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> PFTOOLS_PATH=/var/lib/pftools</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'# OS update'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">DEBIAN_FRONTEND</span><span class="o" style="font-weight: 600;">=</span>noninteractive <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apt-get update <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker"> build-essential <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"> libpcre++-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="docker"> gfortran <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"> libgfortran5 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker"> ca-certificates <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="docker"> git <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="docker"> cmake <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="docker"> zlib1g-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"> libpng-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"> libfile-slurp-perl <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'# Install Pftools V3'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> git clone <span class="nt" style="color: #000080;">--depth</span><span class="o" style="font-weight: 600;">=</span>1 <span class="s2" style="color: #d14;">"https://github.com/sib-swiss/pftools3.git"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">mkdir </span>pftools3/build <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>pftools3/build <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_INSTALL_PREFIX</span>:PATH<span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PFTOOLS_PATH</span> <span class="nt" style="color: #000080;">-DCMAKE_BUILD_TYPE</span><span class="o" style="font-weight: 600;">=</span>Release <span class="nt" style="color: #000080;">-DUSE_GRAPHICS</span><span class="o" style="font-weight: 600;">=</span>OFF <span class="nt" style="color: #000080;">-DUSE_PDF</span><span class="o" style="font-weight: 600;">=</span>ON <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> make <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> make <span class="nb" style="color: #0086b3;">install</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> make <span class="nb" style="color: #0086b3;">test</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: #000080;">-9</span> <span class="nv" style="color: #008080;">$PFTOOLS_PATH</span>/share/man/man5/<span class="k" style="font-weight: 600;">*</span>.5 <span class="nv" style="color: #008080;">$PFTOOLS_PATH</span>/share/man/man1/<span class="k" style="font-weight: 600;">*</span>.1</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:20.04 AS binary</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> PFTOOLS_VERSION</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> BUILD_DATE</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> PFTOOLS_PATH=/var/lib/pftools</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># METADATA</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Use Open Containers Initiative (OCI)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># See https://rehansaeed.com/docker-labels-depth/</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># See https://github.com/opencontainers/image-spec/blob/master/annotations.md</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Exist also another structured label initiative: http://label-schema.org/ superceded by OCI now</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.title="pftools3 - A suite of tools to build and search generalized profiles"</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.version=$PFTOOLS_VERSION</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.vendor="SIB Swiss Institute of Bioinformatics"</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.authors="sebastien.moretti@sib.swiss"</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.url="https://github.com/sib-swiss/pftools3"</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.documentation="https://github.com/sib-swiss/pftools3"</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.licenses="GPL-2.0"</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.description="pftools3 - A suite of tools to build and search generalized profiles"</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> org.opencontainers.image.created=$BUILD_DATE</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="docker"></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #d14;"> --from=compile $PFTOOLS_PATH/ $PFTOOLS_PATH/</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'# OS update'</span> <span class="se" style="color: #d14;">\</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">DEBIAN_FRONTEND</span><span class="o" style="font-weight: 600;">=</span>noninteractive <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apt-get update <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> <span class="se" style="color: #d14;">\</span></span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="docker"> man-db <span class="se" style="color: #d14;">\</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="docker"> ca-certificates <span class="se" style="color: #d14;">\</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="docker"> libfile-slurp-perl <span class="se" style="color: #d14;">\</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="docker"> libc6 <span class="se" style="color: #d14;">\</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="docker"> libgcc1 <span class="se" style="color: #d14;">\</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="docker"> libgfortran5 <span class="se" style="color: #d14;">\</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="docker"> libpcre3 <span class="se" style="color: #d14;">\</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="docker"> libquadmath0 <span class="se" style="color: #d14;">\</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$PFTOOLS_PATH</span>/bin/<span class="k" style="font-weight: 600;">*</span> /usr/local/bin/ <span class="se" style="color: #d14;">\</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$PFTOOLS_PATH</span>/share/man/man5/<span class="k" style="font-weight: 600;">*</span> /usr/share/man/man5/ <span class="se" style="color: #d14;">\</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$PFTOOLS_PATH</span>/share/man/man1/<span class="k" style="font-weight: 600;">*</span> /usr/share/man/man1/ <span class="se" style="color: #d14;">\</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> mandb <span class="se" style="color: #d14;">\</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apt autoremove <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apt-get clean <span class="se" style="color: #d14;">\</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-fr</span> /var/lib/apt/lists/<span class="k" style="font-weight: 600;">*</span> <span class="se" style="color: #d14;">\</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> update-ca-certificates</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="docker"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="docker"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># SECURITY</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">## Control root access</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> USER=pftools3</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>groupadd <span class="nt" style="color: #000080;">-g</span> 1001 <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">&&</span> useradd <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-u</span> 1001 <span class="nt" style="color: #000080;">-g</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="docker"><span class="k" style="font-weight: 600;">USER</span><span class="s" style="color: #d14;"> ${USER}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> HOME=/home/${USER}</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="docker"><span class="k" style="font-weight: 600;">WORKDIR</span><span class="s" style="color: #d14;"> ${HOME}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">##Rest of Dockerfile with this user</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> LC_ALL="C"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="docker"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="docker"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#TODO man pages do not work???</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># TEST</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN for </span>pl <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$PFTOOLS_PATH</span>/bin/<span class="k" style="font-weight: 600;">*</span>.pl<span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>perl <span class="nt" style="color: #000080;">-cw</span> <span class="nv" style="color: #008080;">$pl</span><span class="p">;</span> <span class="k" style="font-weight: 600;">done</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> pfscanV3 <span class="nt" style="color: #000080;">-h</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> pfscan <span class="nt" style="color: #000080;">-h</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> pfsearchV3 <span class="nt" style="color: #000080;">-h</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> pfsearch <span class="nt" style="color: #000080;">-h</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="docker"><span class="k" style="font-weight: 600;">HEALTHCHECK</span><span class="s" style="color: #d14;"> CMD pfscanV3 -h || exit 1</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="docker"><span class="k" style="font-weight: 600;">CMD</span><span class="s" style="color: #d14;"> ["bash"]</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="docker"></span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#59e70f737a878c10c711a056493a7d58029945cc"><strong>Docker/README.docker</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Build Docker image</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker">export PFTOOLS_VERSION=3.2.6</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="docker">docker build -t pftools:$PFTOOLS_VERSION --no-cache=true --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg PFTOOLS_VERSION=$PFTOOLS_VERSION -f Dockerfile . 2>&1 >pftools.Dockerfile.log</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># List Docker local images (imported or built)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker">docker images</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Inspect images</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker">docker inspect pftools:$PFTOOLS_VERSION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Run pfscanV3 in the Docker image</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker">docker run --name pftools --rm -i -t pftools:$PFTOOLS_VERSION pfscanV3</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="docker"></span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,13 +24,12 @@ it was originally published in</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"> A generalized profile syntax for biomolecular sequence motifs</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"> and its function in automatic sequence interpretation.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"> Proc Int Conf Intell Syst Mol Biol. 1994;2:53-61.</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"> PubMed PMID: <span class="p">[</span><span class="nv" style="color: #008080;">7584418</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/pubmed/7584418</span><span class="p">)</span><span class="idiff left right"> </span>.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"> PubMed PMID: <span class="p">[</span><span class="nv" style="color: #008080;">7584418</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/pubmed/7584418</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Command-line tutorial</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">In the doc/example subdirectory, the <span class="p">[</span><span class="nv" style="color: #008080;">test_V3.sh</span><span class="p">](</span><span class="sx" style="color: #d14;">https://raw.githubusercontent.com/sib-swiss/pftools3/master/doc/example/test_V3.sh</span><span class="p">)</span> shell script is a good starting</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">point for using pfsearchV3/pfscanV3</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">After installation, in the share/examples/ subdirectory, the <span class="ge" style="font-style: italic;">*test_V3.sh*</span> shell script is a good starting point for using pfsearchV3/pfscanV3.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Algorithms description</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#43609a23d2d5dd48390d5916d1702758bb3590f5"><strong>src/C/prg/pfscan.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -397,7 +397,7 @@ int main (int argc, char *argv[])</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"> <span class="p">}</span></span>
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399
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ProfileCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"pfscanV3 is not meant to be used with a single profile, use pfsearchV3 to get better performance in such case.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"pfscanV3 is not meant to be used with a single profile, use pfsearchV3 to get better performance in such case.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="idiff left right"> </span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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401
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="p">}</span></span>
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402
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"></span>
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403
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Create an array of pointer to Profiles separating pattern from matrix */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1017,7 +1017,7 @@ int main (int argc, char *argv[])</td>
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1017
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1017
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<pre style="margin: 0;"> <span id="LC1017" 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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1018
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1018
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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"PREFIX profile:<http://example.org/yourprofiledb></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1019
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="c"> <span class="p">}</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="c"></span>
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1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="c"> <span class="p">}</span></span>
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1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Initialize the print mutex */</span></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#4733e34ee0817b24a38b0933ce77ea2d5dddcb57"><strong>src/C/utils/io.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pfProfile.h"</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">NormalizationModeName</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">16</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">NormalizationModeName</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">16</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"> <span class="s" style="color: #d14;">"linear</span><span class="se" style="color: #d14;">\0\0\0\0\0\0\0\0\0\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="s" style="color: #d14;">"gle_zscore</span><span class="se" style="color: #d14;">\0\0\0\0\0\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"> <span class="s" style="color: #d14;">"gle_zscave</span><span class="se" style="color: #d14;">\0\0\0\0\0\0</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,7 +67,7 @@ unsigned int out_profile = 0;</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This structure is fed by the Line Analyzer which parses the input, transforms delimiting symbols</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * into '\0' end character and sets the starting pointer within the ProfileLine structure.</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ProfileLine</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ProfileLine</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">command</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subcommand</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">keywords</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,7 +89,7 @@ static inline size_t GetLine(FILE * const stream, char * const restrict Destinat</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Destination</span><span class="p">[</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="n" style="color: #333;">Destination</span><span class="p">[</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">length</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC93" 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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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +98,7 @@ static inline size_t GetLine(FILE * const stream, char * const restrict Destinat</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">FirstChar</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">MaxMemPoint</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"><span class="p">{</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Line</span><span class="p">;</span><span class="idiff left right"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">Line</span><span class="p">;</span></span>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MaxMemPoint</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +115,7 @@ static inline char * CopyUptoSymbol(char * const restrict Destination, const cha</td>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">Line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Symbol</span><span class="p">){</span></span>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="p">}</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left right"> </span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">Destination</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="p">}</span></span>
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121
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,7 +131,7 @@ static inline char * CopyUptoSymbolTerminated(char * const restrict Destination,</td>
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131
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">Destination</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="p">}</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="idiff left right"> </span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">Destination</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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136
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="p">}</span></span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">Destination</span><span class="p">[</span><span class="n" style="color: #333;">MaxLength</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -219,7 +219,7 @@ static inline size_t CountAndReplaceSymbol(char * const restrict String, const c</td>
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219
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _DEBUG_VERBOSE_</span></span>
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220
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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221
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c"> <span class="p">}</span></span>
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223
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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224
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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225
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -262,7 +262,7 @@ static inline size_t CountSymbol(const char * const restrict String, const char</td>
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262
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _DEBUG_VERBOSE_</span></span>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c"> <span class="p">}</span></span>
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266
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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268
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -281,7 +281,7 @@ static int AnalyzeLine(char * restrict currentLine, struct ProfileLine * const r</td>
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281
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">MaxMemPoint</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">currentLine</span><span class="p">[</span><span class="n" style="color: #333;">LineSize</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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282
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _VERBOSE_</span></span>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_profile</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UseColor</span><span class="p">)</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UseColor</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"\e[31;40mLine : %s\e[0m</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Line : %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -289,7 +289,7 @@ static int AnalyzeLine(char * restrict currentLine, struct ProfileLine * const r</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Set Multiple line to false */</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MultipleLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Clear result first */</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">prfLine</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ProfileLine</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">SUB_COMMAND_MAX_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -298,7 +298,7 @@ static int AnalyzeLine(char * restrict currentLine, struct ProfileLine * const r</td>
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">prfLine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Position</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">_Bool</span> <span class="n" style="color: #333;">isMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Position</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">Position</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">prfLine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isMatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"></span>
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Get to end of command and replace space by '\0' */</span></span>
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<pre style="margin: 0;"> <span id="LC303" 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;">Position</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">Position</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxMemPoint</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Position</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC304" 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;">Position</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span><span class="n" style="color: #333;">Position</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">MaxMemPoint</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Position</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,12 +321,12 @@ static int AnalyzeLine(char * restrict currentLine, struct ProfileLine * const r</td>
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<pre style="margin: 0;"> <span id="LC321" 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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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _VERBOSE_</span></span>
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_profile</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UseColor</span><span class="p">)</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UseColor</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" \e[31;40mMULTIPLE MA LINES DETECTED\e[0m"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" MULTIPLE MA LINES DETECTED"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="c"> <span class="n" style="color: #333;">prfLine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">subcommand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">previousSubCommand</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MultipleLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -432,12 +432,12 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="c"> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="n" style="color: #333;">IIPD_BOUNDARIES</span> <span class="p">[</span> <span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">aligned</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="c"> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="n" style="color: #333;">IMPD_ALPHABET</span> <span class="p">[</span> <span class="n" style="color: #333;">ALPHABET_MEMORY_SIZE</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">aligned</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="c"> <span class="n" style="color: #333;">TransitionScores</span> <span class="n" style="color: #333;">IIPD_TRANSITIONS</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">aligned</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">currentLine</span><span class="p">[</span><span class="n" style="color: #333;">PROFILE_MAX_LINE_SIZE</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">aligned</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ProfileLine</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="c"> <span class="k" style="font-weight: 600;">union</span> <span class="n" style="color: #333;">Scores</span> <span class="n" style="color: #333;">DefaultScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="c"> <span class="k" style="font-weight: 600;">union</span> <span class="n" style="color: #333;">Scores</span> <span class="n" style="color: #333;">DefaultScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="c"> <span class="n" style="color: #333;">Insertion</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">{</span> <span class="n" style="color: #333;">IIPD_ALPHABET</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">IIPD_BOUNDARIES</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">IIPD_TRANSITIONS</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -449,7 +449,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="c"> <span class="k" style="font-weight: 600;">union</span> <span class="n" style="color: #333;">Scores</span> <span class="n" style="color: #333;">WorkingScores</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ProfileSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">Line</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">LineOffset</span><span class="p">,</span> <span class="n" style="color: #333;">Alphabet_Length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">Length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">InsertionCounter</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;">MatchCounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">_Bool</span> <span class="n" style="color: #333;">LZCO</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -457,24 +457,24 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">DefaultMatchSymbol</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">DefaultInsertionSymbol</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Initialize position-independent profile parameters</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * - general specification</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isCircular</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="c"><span class="idiff left right"> </span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isReversed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"><span class="idiff left right"> </span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isReversed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* - disjoint mode */</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">MDIS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">CDIS</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">"UNIQUE</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">CDIS</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"PROTECT</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">JDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">JDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* - normalization modes */</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">NormalizationData</span><span class="p">.</span><span class="n" style="color: #333;">JNOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -492,22 +492,22 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* - cut-off */</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CutOffData</span><span class="p">.</span><span class="n" style="color: #333;">JCUT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Pattern */</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="c"> <span class="n" style="color: #333;">InitializeDefault</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">DefaultScores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">DefaultMatchSymbol</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">DefaultInsertionSymbol</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">previousSubCommand</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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;">char</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">SUB_COMMAND_MAX_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Read profile</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _VERBOSE_</span></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">_Bool</span> <span class="n" style="color: #333;">FirstCall</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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508
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="c"><span class="idiff left right"> </span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">))</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"></span>
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510
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<pre style="margin: 0;">+<span id="LC510" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">))</span> <span class="p">{</span></span>
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511
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetLine</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="n" style="color: #333;">PROFILE_MAX_LINE_SIZE</span><span class="p">);</span></span>
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512
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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513
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Line</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -530,7 +530,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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530
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Error %i in analysis at line %lu</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">);</span></span>
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531
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531
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<pre style="margin: 0;"> <span id="LC531" 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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<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Header or matrix */</span></span>
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535
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<pre style="margin: 0;"> <span id="LC535" 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;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">isMatrix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -543,9 +543,9 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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543
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PF_PATTERN</span><span class="p">;</span></span>
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="c"> <span class="p">}</span></span>
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545
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MissingType</span><span class="p">;</span><span class="idiff left right"> </span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MissingType</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'A'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="c"> <span class="n" style="color: #333;">CopyUptoSymbol</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AC_Number</span><span class="p">,</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">subcommand</span><span class="p">,</span> <span class="sc" style="color: #d14;">';'</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -623,17 +623,17 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="c"> <span class="n" style="color: #333;">Alphabet_Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALPHABET_SIZE</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Alphabet_Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Alphabet_Length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">keywords</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="s" style="color: #d14;">"LENGTH"</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"> <span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Allocates memory</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="n" style="color: #333;">Length</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">AllocationError</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"> <span class="n" style="color: #333;">ProfileSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">ProfileSequence</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">Length</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="c"></span>
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637
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">AllocateScores</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">WorkingScores</span><span class="p">,</span> <span class="n" style="color: #333;">Alphabet_Length</span><span class="p">,</span> <span class="n" style="color: #333;">Length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">AllocationError</span><span class="p">;</span></span>
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"></span>
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Copy score pointers to profile */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -677,7 +677,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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677
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">JNOR</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">MAXN</span><span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">TooManyNormalization</span><span class="p">;</span></span>
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678
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="n" style="color: #333;">SNormalizationItem</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">nrmItem</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">nrm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Values</span><span class="p">[</span><span class="n" style="color: #333;">JNOR</span><span class="p">]);</span></span>
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679
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="c"> <span class="n" style="color: #333;">nrmItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CNTX</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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680
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="c"></span>
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">counter</span><span class="p">;</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">keys</span><span class="p">)</span> <span class="p">{</span></span>
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682
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">keywords</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="s" style="color: #d14;">"FUNCTION"</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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683
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ctmp</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GRIBSKOV"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -718,14 +718,14 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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718
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">endptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">)</span> <span class="p">{</span></span>
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719
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Line %lu : unable to convert %s to float</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">]);</span></span>
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720
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720
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<pre style="margin: 0;"> <span id="LC720" 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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721
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="c"> <span class="p">}</span></span>
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722
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">endptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">]</span> <span class="p">)</span> <span class="p">{</span></span>
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723
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Line %lu : conversion error of %s to float</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="c"> <span class="s" style="color: #d14;">" : error code %i = %s"</span><span class="p">,</span></span>
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725
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="c"> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="n" style="color: #333;">errno</span><span class="p">,</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="c"><span class="idiff left right"> </span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="c"></span>
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727
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<pre style="margin: 0;"> <span id="LC727" 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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<pre style="margin: 0;">-<span id="LC728" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="c"> <span class="p">}</span></span>
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729
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -760,7 +760,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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760
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">MaxMemory</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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761
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">CountAndReplaceSymbol</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="n" style="color: #333;">MaxMemory</span><span class="p">);</span></span>
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762
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">MAXN</span><span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">TooManyScores</span><span class="p">;</span></span>
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763
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="c"><span class="idiff left right"> </span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="c"></span>
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764
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">count</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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765
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">newpos</span><span class="p">;</span></span>
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766
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="c"> <span class="n" style="color: #333;">ctItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">RCUT</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtof</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">newpos</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -769,7 +769,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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769
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769
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<pre style="margin: 0;"> <span id="LC769" 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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770
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c"> <span class="p">}</span></span>
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771
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771
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<pre style="margin: 0;"> <span id="LC771" 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;">newpos</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">newpos</span><span class="p">;</span></span>
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772
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="idiff left right"> </span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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773
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="c"> <span class="p">}</span></span>
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774
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="c"> <span class="n" style="color: #333;">ctItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">JCNM</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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775
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">keywords</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="s" style="color: #d14;">"MODE"</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -798,14 +798,14 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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798
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'S'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'Y'</span><span class="p">)</span> <span class="p">{</span></span>
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799
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">)</span> <span class="p">{</span></span>
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800
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="c"> <span class="n" style="color: #333;">DefaultMatchSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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801
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="c"> <span class="p">}</span></span>
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802
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">)</span> <span class="p">{</span></span>
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803
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="c"> <span class="n" style="color: #333;">DefaultInsertionSymbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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804
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="c"> <span class="p">}</span></span>
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805
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="c"> <span class="p">}</span></span>
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806
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span> <span class="p">)</span> <span class="p">{</span></span>
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807
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">ReadScore</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">DefaultScores</span><span class="p">.</span><span class="n" style="color: #333;">Match</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ReadError</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="c"> <span class="p">}</span></span>
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809
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\0'</span> <span class="p">)</span> <span class="p">{</span></span>
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810
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">];</span></span>
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811
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">MaxMemory</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">)</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -814,7 +814,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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814
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="c"> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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815
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">ReadScore</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ReadError</span><span class="p">;</span></span>
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816
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Alphabet_Length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">DefaultScores</span><span class="p">.</span><span class="n" style="color: #333;">Match</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="c"> <span class="p">}</span></span>
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">ReadScores</span><span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">DefaultScores</span><span class="p">.</span><span class="n" style="color: #333;">Match</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">count</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ReadError</span><span class="p">;</span></span>
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -883,7 +883,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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883
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Read the scores */</span></span>
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884
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">counter</span><span class="p">;</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">keys</span><span class="p">)</span> <span class="p">{</span></span>
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885
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">keywords</span><span class="p">[</span><span class="n" style="color: #333;">keys</span><span class="p">];</span></span>
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886
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'S'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'Y'</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span><span class="idiff left right"> </span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'S'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">key</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'Y'</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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887
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="c"> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="p">;</span></span>
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888
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetInsertionMemory</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">WorkingScores</span><span class="p">.</span><span class="n" style="color: #333;">Insertion</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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889
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">type</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -927,7 +927,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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927
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf(stderr, "Line %lu : implicit Insertion : %lu <= %lu\n", Line, InsertionCounter, MatchCounter);</span></span>
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928
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _VERBOSE_</span></span>
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929
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_profile</span><span class="p">)</span> <span class="p">{</span></span>
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930
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UseColor</span><span class="p">)</span><span class="idiff left right"> </span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UseColor</span><span class="p">)</span></span>
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931
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="c"> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">" \e[0;32m IMPLICIT INSERTION OF I\e[0m</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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932
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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933
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="c"> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">" IMPLICIT INSERTION OF I</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -938,7 +938,7 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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938
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">WorkingScores</span><span class="p">.</span><span class="n" style="color: #333;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Transitions</span><span class="p">,</span> <span class="n" style="color: #333;">DefaultScores</span><span class="p">.</span><span class="n" style="color: #333;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Transitions</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">TransitionScores</span><span class="p">));</span></span>
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939
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939
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<pre style="margin: 0;"> <span id="LC939" class="line" lang="c"></span>
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940
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940
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// CopyPreviousInsertionProfile(&WorkingScores.Insertion);</span></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="c"><span class="idiff left right"> </span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="c"></span>
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942
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942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="c"> <span class="n" style="color: #333;">NextInsertionProfile</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">WorkingScores</span><span class="p">.</span><span class="n" style="color: #333;">Insertion</span><span class="p">);</span></span>
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943
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">InsertionCounter</span><span class="p">;</span></span>
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944
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -992,14 +992,14 @@ static int internalReadProfile(FILE* prfStream, struct Profile * const prf, cons</td>
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * End of file reached without end of profile keyword. This typically happens when profile</span></span>
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * has empty lines after the last end of profile keyword.</span></span>
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Let us check this and return here with special value -1.</span></span>
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="c"><span class="nl">END_OF_PROFILE:</span></span>
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PF_MATRIX</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Insert possible missing I when profile starts with M */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1011,7 +1011,7 @@ END_OF_PROFILE:</td>
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">InsertionCounter</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">SetExtraTable</span><span class="p">)</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">SetExtraTable</span><span class="p">)</span></span>
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1015
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="c"> <span class="p">{</span></span>
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1016
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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1017
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1017
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PrepareExtraTable</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1022,7 +1022,7 @@ END_OF_PROFILE:</td>
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1022
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<td class="new_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Copy default values */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">WorkingScores</span><span class="p">.</span><span class="n" style="color: #333;">Match</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">,</span> <span class="n" style="color: #333;">DefaultScores</span><span class="p">.</span><span class="n" style="color: #333;">Match</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ALPHABET_MEMORY_SIZE</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">StoredIntegerFormat</span><span class="p">));</span></span>
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1024
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="c"> <span class="p">}</span></span>
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1025
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="c"></span>
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1026
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1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* CHECK CONSISTENCY */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">MatchCounter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Length</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">MatchCounter</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Length</span> <span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1059,7 +1059,7 @@ END_OF_PROFILE:</td>
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1059
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1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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1060
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="c"> <span class="s" style="color: #d14;">"Warning: Disjointness parameter 2 (%i) out of bound. Parameter set to acceptable value.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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1062
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<td class="new_line diff-line-num old" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1062" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Length</span><span class="p">;</span><span class="idiff left right"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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1063
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="c"> <span class="p">}</span></span>
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1064
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="c"></span>
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1065
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1068,18 +1068,18 @@ END_OF_PROFILE:</td>
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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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1069
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="c"> <span class="p">}</span></span>
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1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="c"> <span class="p">}</span></span>
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1071
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<pre style="margin: 0;">-<span id="LC1071" class="line" lang="c"><span class="idiff left right"> </span></span>
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1071
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1072
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1072
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">LineOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Line</span><span class="p">;</span></span>
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1073
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1073
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<pre style="margin: 0;"> <span id="LC1073" 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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1074
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<pre style="margin: 0;">-<span id="LC1074" class="line" lang="c"><span class="idiff left right"> </span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="c"></span>
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1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1076
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1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * ERRORS</span></span>
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="c"><span class="idiff left right"> </span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="c"></span>
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1079
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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// MissingSymbol:</span></span>
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1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf(stderr, "Missing symbol %c at line %lu of %s\n\tLine: %s\n",Symbol,Line, FileName, prfLine);</span></span>
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1081
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1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// return 1;</span></span>
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<pre style="margin: 0;">-<span id="LC1082" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="c"><span class="nl">MissingType:</span></span>
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1084
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Identification</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="p">{</span></span>
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Missing MATRIX or PATTERN keyword at line %lu of profile %s</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Line: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Identification</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1087,7 +1087,7 @@ MissingType:</td>
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1087
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1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Missing MATRIX or PATTERN keyword at line %lu of %s</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Line: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">FileName</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">);</span></span>
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1088
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1088
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="c"> <span class="p">}</span></span>
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1089
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1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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1090
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<pre style="margin: 0;">-<span id="LC1090" class="line" lang="c"><span class="idiff left right"> </span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="c"></span>
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1091
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="c"><span class="nl">AlphabetSizeTooLarge:</span></span>
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1092
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alphabet size exceeds hard defined size: %u > %lu</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ALPHABET_SIZE</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Alphabet_Length</span><span class="p">);</span></span>
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1093
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1093
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1097,9 +1097,9 @@ NormalizationError:</td>
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1097
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="c"> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">FileName</span><span class="p">);</span></span>
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1098
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">KNOR</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s "</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">NormalizationData</span><span class="p">.</span><span class="n" style="color: #333;">CNOR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1099
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1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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1100
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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="c"><span class="idiff left right"> </span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="c"></span>
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1101
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1101
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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="c"><span class="idiff left right"> </span></span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="c"></span>
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1103
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="c"><span class="nl">TooManyNormalization:</span></span>
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1104
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Too many normalization parameters at line %lu of %s</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Maximum is %i.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">FileName</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1105
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1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1128,14 +1128,14 @@ AllocationError:</td>
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1128
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to allocate sufficient memory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1129
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1129
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span><span class="p">);</span></span>
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1130
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<td class="new_line diff-line-num" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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1131
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<td class="new_line diff-line-num old" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1131" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="c"></span>
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1132
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<td class="new_line diff-line-num" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="c"><span class="nl">WrongType:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
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<td class="new_line diff-line-num" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"MA keyword should not appear in PATTERN profile at line %lu of %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">FileName</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1134
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<td class="new_line diff-line-num" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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1135
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<td class="new_line diff-line-num old" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="c"></span>
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1136
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<td class="new_line diff-line-num" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="c"><span class="nl">NoLength:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1137
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<td class="new_line diff-line-num" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Profile does not bear a LENGTH in GENERAL_SPEC option at line %lu of %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">,</span> <span class="n" style="color: #333;">FileName</span><span class="p">);</span></span>
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1138
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<td class="new_line diff-line-num old" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="c"></span>
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1139
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<td class="new_line diff-line-num" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="c"><span class="nl">FIN:</span></span>
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1140
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1140
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<pre style="margin: 0;"> <span id="LC1140" 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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1141
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1150,17 +1150,17 @@ static int ComplementAlphabet(struct Profile * const prf)</td>
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1150
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> Alphabet_Mapping[x - (unsigned char) 'A'] = Alphabet_Mapping[y - (unsigned char) 'A'];\</span></span>
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1151
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<td class="new_line diff-line-num" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> Alphabet_Mapping[y - (unsigned char) 'A'] = ctmp;\</span></span>
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1152
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1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">}</span></span>
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1153
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<td class="new_line diff-line-num old" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1153" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Complement_Alphabet_Mapping</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Alphabet_Mapping</span><span class="p">,</span> <span class="n" style="color: #333;">ALPHABET_SIZE</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span><span class="idiff left right"> </span></span>
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1154
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<td class="new_line diff-line-num old" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1154" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PF_MATRIX</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Complement_Alphabet_Mapping</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Alphabet_Mapping</span><span class="p">,</span> <span class="n" style="color: #333;">ALPHABET_SIZE</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PF_MATRIX</span><span class="p">)</span> <span class="p">{</span></span>
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1155
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1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="c"> <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="k" style="font-weight: 600;">const</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">Alphabet_Mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Complement_Alphabet_Mapping</span><span class="p">;</span></span>
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1156
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<pre style="margin: 0;">-<span id="LC1156" class="line" lang="c"><span class="idiff left right"> </span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="c"></span>
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1157
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1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="c"> <span class="n" style="color: #333;">SWAP_ALPHABET</span><span class="p">(</span><span class="sc" style="color: #d14;">'A'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'T'</span><span class="p">);</span></span>
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1158
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1158
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<pre style="margin: 0;"> <span id="LC1158" class="line" lang="c"> <span class="n" style="color: #333;">SWAP_ALPHABET</span><span class="p">(</span><span class="sc" style="color: #d14;">'C'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">);</span></span>
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1159
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1159
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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="c"> <span class="n" style="color: #333;">SWAP_ALPHABET</span><span class="p">(</span><span class="sc" style="color: #d14;">'M'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'K'</span><span class="p">);</span></span>
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1160
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="c"> <span class="n" style="color: #333;">SWAP_ALPHABET</span><span class="p">(</span><span class="sc" style="color: #d14;">'R'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'Y'</span><span class="p">);</span></span>
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1161
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1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="c"> <span class="n" style="color: #333;">SWAP_ALPHABET</span><span class="p">(</span><span class="sc" style="color: #d14;">'V'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'B'</span><span class="p">);</span></span>
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1162
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1162
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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="c"> <span class="n" style="color: #333;">SWAP_ALPHABET</span><span class="p">(</span><span class="sc" style="color: #d14;">'H'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'D'</span><span class="p">);</span></span>
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1163
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<pre style="margin: 0;">-<span id="LC1163" class="line" lang="c"><span class="idiff left right"> </span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="c"></span>
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1164
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1164
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<pre style="margin: 0;"> <span id="LC1164" 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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1165
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="c"> <span class="p">}</span></span>
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1166
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1206,7 +1206,7 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1206
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1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="c"> <span class="n" style="color: #333;">ScoreTuple</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">LastSequenceProtein</span><span class="p">;</span></span>
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1207
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1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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1208
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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1209
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<pre style="margin: 0;">-<span id="LC1209" class="line" lang="c"><span class="idiff left right"> </span></span>
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1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="c"></span>
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1210
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1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isCircular</span><span class="p">)</span> <span class="p">{</span></span>
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1211
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1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">Length</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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1212
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INSERTION_TRANSITIONS_SIZE</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1217,13 +1217,13 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1217
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1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<td class="new_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<td class="new_line diff-line-num" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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1220
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<pre style="margin: 0;">-<span id="LC1220" class="line" lang="c"><span class="idiff left right"> </span></span>
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1221
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<pre style="margin: 0;">-<span id="LC1221" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="c"></span>
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1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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1222
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1223
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1223
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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E0</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1224
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1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E0</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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1225
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1225
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<pre style="margin: 0;"> <span id="LC1225" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E0</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DE</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC1226" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">FirstScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">]</span> <span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B0</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1228
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1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">FirstScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B0</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1229
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1229
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<pre style="margin: 0;"> <span id="LC1229" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">FirstScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]</span> <span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B0</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1232,11 +1232,11 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1232
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1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">LastScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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1233
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1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">LastScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]</span> <span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DE</span><span class="p">]);</span></span>
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1234
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1234
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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="c"> <span class="p">}</span></span>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="c"> <span class="p">}</span></span>
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1236
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1236
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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1237
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1237
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">NDIP1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1238
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1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">NDIP2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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1239
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<pre style="margin: 0;">-<span id="LC1239" class="line" lang="c"><span class="idiff left right"> </span></span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="c"></span>
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1240
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">NDIP1</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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1241
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INSERTION_TRANSITIONS_SIZE</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1242
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1244,8 +1244,8 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1245
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1246
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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1247
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<pre style="margin: 0;">-<span id="LC1247" class="line" lang="c"><span class="idiff left right"> </span></span>
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1248
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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="c"></span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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1249
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1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1250
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1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1251
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1266,8 +1266,8 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1266
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1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1267
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1268
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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1269
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<pre style="margin: 0;">-<span id="LC1269" class="line" lang="c"><span class="idiff left right"> </span></span>
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1270
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<pre style="margin: 0;">-<span id="LC1270" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1272
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1272
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1273
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1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1288,8 +1288,8 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1288
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1288
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1289
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1290
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1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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1291
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<pre style="margin: 0;">-<span id="LC1291" class="line" lang="c"><span class="idiff left right"> </span></span>
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1292
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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1294
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1294
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1295
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1324,15 +1324,15 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="c"> <span class="n" style="color: #333;">ScoreTuple</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastScores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">LastSequenceProtein</span><span class="p">;</span></span>
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1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1327" class="line" lang="c"><span class="idiff left right"> </span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="c"></span>
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1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isCircular</span><span class="p">)</span> <span class="p">{</span></span>
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1329
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1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"No coverage on circular profile"</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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1330
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1330
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<pre style="margin: 0;"> <span id="LC1330" 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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1331
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<pre style="margin: 0;">-<span id="LC1331" class="line" lang="c"> <span class="p">}</span><span class="idiff left right"> </span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="c"> <span class="p">}</span></span>
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1332
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1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1333
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1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">NDIP1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1334
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1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">NDIP2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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1335
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<pre style="margin: 0;">-<span id="LC1335" class="line" lang="c"><span class="idiff left right"> </span></span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="c"></span>
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1336
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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">NDIP1</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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1337
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INSERTION_TRANSITIONS_SIZE</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1338
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1340,8 +1340,8 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1341
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1342
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC1343" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC1344" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1346
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1347
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1362,8 +1362,8 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1362
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1363
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1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1364
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1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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1365
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<pre style="margin: 0;">-<span id="LC1365" class="line" lang="c"><span class="idiff left right"> </span></span>
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1366
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<pre style="margin: 0;">-<span id="LC1366" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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1367
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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1368
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1369
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1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1384,8 +1384,8 @@ int PrepareExtraTable(struct Profile * const prf)</td>
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1384
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1384
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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XM</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BM</span><span class="p">]);</span></span>
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1385
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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XI</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BI</span><span class="p">]);</span></span>
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1386
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1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_XD</span><span class="p">],</span> <span class="n" style="color: #333;">NLOW</span><span class="p">,</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_BD</span><span class="p">]);</span></span>
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1387
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<td class="new_line diff-line-num old" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1387" class="line" lang="c"><span class="idiff left right"> </span></span>
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1388
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<td class="new_line diff-line-num old" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1388" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element<span class="idiff left right"> </span></span></span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="c"></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Minimize dummy element</span></span>
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1389
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1389
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<pre style="margin: 0;"> <span id="LC1389" class="line" lang="c"> <span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_DUMMY</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NLOW</span><span class="p">;</span></span>
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1390
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_MX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_ME</span><span class="p">]);</span></span>
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1391
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1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="c"> <span class="n" style="color: #333;">CHECK_AND_SET</span><span class="p">(</span><span class="n" style="color: #333;">InsertionScores</span><span class="p">[</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IX</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_E1</span><span class="p">],</span> <span class="n" style="color: #333;">InsertionBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">Boffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_IE</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1412,7 +1412,7 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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1412
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1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Profile</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">outprf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Profile</span><span class="p">),</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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1413
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1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outprf</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1414
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">prfLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span><span class="p">;</span></span>
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1415
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="c"><span class="idiff left right"> </span></span>
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1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="c"></span>
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1416
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1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Copy parameters */</span></span>
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1417
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1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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1418
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1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">outprf</span><span class="p">,</span> <span class="n" style="color: #333;">inprf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Profile</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1431,7 +1431,7 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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1431
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1431
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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1432
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1432
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<pre style="margin: 0;"> <span id="LC1432" class="line" lang="c"> <span class="n" style="color: #333;">outprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">prfLength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">inprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1433
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1433
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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="c"> <span class="n" style="color: #333;">outprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">prfLength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">inprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DisjointData</span><span class="p">.</span><span class="n" style="color: #333;">NDIP</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1434
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<pre style="margin: 0;">-<span id="LC1434" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="c"></span>
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1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Allocates memory for profile sequence */</span></span>
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1436
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1436
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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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1437
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1437
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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1442,14 +1442,14 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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1442
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1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">prfLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iprf</span><span class="p">)</span> <span class="p">{</span></span>
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1443
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1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="c"> <span class="n" style="color: #333;">Sequence</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">];</span></span>
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1444
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="c"> <span class="p">}</span></span>
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1445
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<pre style="margin: 0;">-<span id="LC1445" class="line" lang="c"><span class="idiff left right"> </span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="c"></span>
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1446
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1446
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Allocates memory for score tables*/</span></span>
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1447
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1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">AllocateScores</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">outprf</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;">inprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Alphabet_Length</span><span class="p">,</span> <span class="n" style="color: #333;">prfLength</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1448
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1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">);</span></span>
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1449
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1449
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="c"> <span class="n" style="color: #333;">_mm_free</span><span class="p">(</span><span class="n" style="color: #333;">outprf</span><span class="p">);</span></span>
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1450
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1450
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<pre style="margin: 0;"> <span id="LC1450" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1451
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1451
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1452" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1453" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Transfer match and insertion alphabets */</span></span>
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1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="c"> <span class="p">{</span></span>
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1455
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1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">AlignedStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">AlignStep</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1460,7 +1460,7 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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1460
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1460
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<pre style="margin: 0;"> <span id="LC1460" class="line" lang="c"> <span class="n" style="color: #333;">outMatch</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">AlignedStep</span><span class="p">;</span></span>
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1461
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1461
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="c"> <span class="n" style="color: #333;">inMatch</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">AlignedStep</span><span class="p">;</span></span>
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1462
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1462
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<pre style="margin: 0;"> <span id="LC1462" class="line" lang="c"> <span class="p">}</span></span>
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1463
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<pre style="margin: 0;">-<span id="LC1463" class="line" lang="c"><span class="idiff left right"> </span></span>
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1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="c"></span>
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1464
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1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">inInsertion</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">inprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">[</span><span class="n" style="color: #333;">AlignedStep</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">inprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span><span class="p">)];</span></span>
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1465
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1465
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">outInsertion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Alphabet</span><span class="p">;</span></span>
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1466
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1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">prfLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iprf</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="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1469,7 +1469,7 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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1469
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<pre style="margin: 0;"> <span id="LC1469" class="line" lang="c"> <span class="n" style="color: #333;">inInsertion</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">AlignedStep</span><span class="p">;</span></span>
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1470
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1470
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<pre style="margin: 0;"> <span id="LC1470" class="line" lang="c"> <span class="p">}</span></span>
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1471
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1471
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<pre style="margin: 0;"> <span id="LC1471" class="line" lang="c"> <span class="p">}</span></span>
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1472
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<pre style="margin: 0;">-<span id="LC1472" class="line" lang="c"><span class="idiff left right"> </span></span>
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1472
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="c"></span>
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1473
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1473
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<pre style="margin: 0;"> <span id="LC1473" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Transfer boundaries */</span></span>
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1474
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1474
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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inBoundaries</span><span class="p">)[</span><span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">)[</span><span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="p">])</span> <span class="n" style="color: #333;">inprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Boundaries</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outBoundaries</span><span class="p">)[</span><span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">)[</span><span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span><span class="p">])</span> <span class="n" style="color: #333;">outprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Boundaries</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1484,9 +1484,9 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="c"> <span class="n" style="color: #333;">outBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_ME</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BM</span><span class="p">];</span></span>
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1485
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1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="c"> <span class="n" style="color: #333;">outBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BD</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_DE</span><span class="p">];</span></span>
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1486
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1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="c"> <span class="n" style="color: #333;">outBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_DE</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BD</span><span class="p">];</span></span>
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1487
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<pre style="margin: 0;">-<span id="LC1487" class="line" lang="c"> <span class="n" style="color: #333;">outBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BE</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BE</span><span class="p">];</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1487" class="line" lang="c"> <span class="n" style="color: #333;">outBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BE</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inBoundaries</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">][</span><span class="n" style="color: #333;">_BE</span><span class="p">];</span></span>
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1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="c"> <span class="p">}</span></span>
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1489
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<pre style="margin: 0;">-<span id="LC1489" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Transfer transitions */</span></span>
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1491
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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TransitionScores</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inTransitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TransitionScores</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">inprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Transitions</span><span class="p">;</span></span>
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1492
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<pre style="margin: 0;"> <span id="LC1492" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="n" style="color: #333;">TransitionScores</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outTransitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TransitionScores</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">outprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Transitions</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1494,11 +1494,11 @@ struct Profile * ReverseProfile(const struct Profile * const restrict inprf)</td>
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1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_DD</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_DD</span><span class="p">];</span></span>
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1495
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1495
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_DI</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_ID</span><span class="p">];</span></span>
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1496
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1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_DM</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_MD</span><span class="p">];</span></span>
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1497
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<pre style="margin: 0;">-<span id="LC1497" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="c"></span>
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1498
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<td class="new_line diff-line-num" data-linenumber="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1498
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<pre style="margin: 0;"> <span id="LC1498" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_MD</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_DM</span><span class="p">];</span></span>
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1499
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1499
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<pre style="margin: 0;"> <span id="LC1499" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_MM</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_MM</span><span class="p">];</span></span>
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1500
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1500
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<pre style="margin: 0;"> <span id="LC1500" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_MI</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_IM</span><span class="p">];</span></span>
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1501
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<td class="new_line diff-line-num old" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1501" class="line" lang="c"><span class="idiff left right"> </span></span>
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1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="c"></span>
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1502
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1502
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<pre style="margin: 0;"> <span id="LC1502" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_ID</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_DI</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1503
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1503
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<pre style="margin: 0;"> <span id="LC1503" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_IM</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_MI</span><span class="p">];</span></span>
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<td class="old_line diff-line-num" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1504
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1504
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<pre style="margin: 0;"> <span id="LC1504" class="line" lang="c"> <span class="n" style="color: #333;">outTransitions</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_II</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inTransitions</span><span class="p">[</span><span class="n" style="color: #333;">prfLength</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">Element</span><span class="p">[</span><span class="n" style="color: #333;">_II</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1522,13 +1522,13 @@ int ReadProfile(const char * const restrict FileName, struct Profile * const prf</td>
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1522
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1522
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prfStream</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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1523
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1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1524
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1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="c"> <span class="p">}</span></span>
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1525
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<pre style="margin: 0;">-<span id="LC1525" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="c"></span>
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1526
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1526
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<pre style="margin: 0;"> <span id="LC1526" 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="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1527
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<pre style="margin: 0;">-<span id="LC1527" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Read all internal data<span class="idiff left right"> </span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Read all internal data</span></span>
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1528
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1528
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<pre style="margin: 0;"> <span id="LC1528" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1529
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1529
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<pre style="margin: 0;"> <span id="LC1529" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Clean Profile structure */</span></span>
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1530
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1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">newPrf</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Profile</span><span class="p">));</span></span>
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1531
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<pre style="margin: 0;">-<span id="LC1531" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">))</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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1531
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<pre style="margin: 0;">+<span id="LC1531" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">))</span> <span class="p">{</span></span>
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1532
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1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Read one profile structure at a time*/</span></span>
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<td class="old_line diff-line-num" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1533
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1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">internalReadProfile</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">,</span> <span class="n" style="color: #333;">newPrf</span><span class="p">,</span> <span class="n" style="color: #333;">SetExtraTable</span><span class="p">,</span> <span class="n" style="color: #333;">FileName</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Line</span><span class="p">);</span></span>
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1534
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1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nprf</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1541,7 +1541,7 @@ int ReadProfile(const char * const restrict FileName, struct Profile * const prf</td>
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1541
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1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmpPrf</span><span class="p">)</span> <span class="p">{</span></span>
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1542
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1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Clean Profile structure */</span></span>
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1543
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1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">tmpPrf</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Profile</span><span class="p">));</span></span>
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1544
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<pre style="margin: 0;">-<span id="LC1544" class="line" lang="c"><span class="idiff left right"> </span></span>
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1544
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="c"></span>
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1545
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1545
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<pre style="margin: 0;"> <span id="LC1545" class="line" lang="c"> <span class="n" style="color: #333;">tmpPrf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">previous</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newPrf</span><span class="p">;</span></span>
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1546
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1546
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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="c"> <span class="n" style="color: #333;">newPrf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpPrf</span><span class="p">;</span></span>
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1547
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1547
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="c"> <span class="n" style="color: #333;">newPrf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpPrf</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1562,15 +1562,15 @@ int ReadProfile(const char * const restrict FileName, struct Profile * const prf</td>
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1562
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1562
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1563
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<pre style="margin: 0;"> <span id="LC1563" class="line" lang="c"> <span class="n" style="color: #333;">nprf</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1564
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<pre style="margin: 0;"> <span id="LC1564" class="line" lang="c"> <span class="p">}</span></span>
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1565
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<pre style="margin: 0;">-<span id="LC1565" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span><span class="idiff left right"> </span></span>
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1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1566
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1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="c"> <span class="p">}</span></span>
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1567
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1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1568" class="line" lang="c"><span class="idiff left right"> </span></span>
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1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1570
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<pre style="margin: 0;">-<span id="LC1570" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Close the file<span class="idiff left right"> </span></span></span>
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1570
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Close the file</span></span>
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1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1572
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1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span></span>
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1573
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<pre style="margin: 0;">-<span id="LC1573" class="line" lang="c"><span class="idiff left right"> </span></span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nprf</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1575" class="line" lang="c"><span class="p">}</span></span>
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1576
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1598,9 +1598,9 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1598
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<pre style="margin: 0;"> <span id="LC1598" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prfStreamIn</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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1599
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<pre style="margin: 0;"> <span id="LC1599" 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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1600
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1600
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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1601" class="line" lang="c"><span class="idiff left right"> </span></span>
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1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="c"></span>
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1602
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<pre style="margin: 0;"> <span id="LC1602" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC1603" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Write down the header data<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Write down the header data</span></span>
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1604
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1604
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<pre style="margin: 0;"> <span id="LC1604" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1605
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1605
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<pre style="margin: 0;"> <span id="LC1605" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamOut</span><span class="p">,</span></span>
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1606
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="c"> <span class="s" style="color: #d14;">"ID %s; MATRIX.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1609,7 +1609,7 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1609
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1609
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<pre style="margin: 0;"> <span id="LC1609" class="line" lang="c"> <span class="s" style="color: #d14;">"DE %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1610
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1610
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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="c"> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Identification</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AC_Number</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Date</span><span class="p">,</span> <span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Description</span></span>
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1611
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1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="c"> <span class="p">);</span></span>
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1612
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<pre style="margin: 0;">-<span id="LC1612" class="line" lang="c"><span class="idiff left right"> </span></span>
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1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="c"></span>
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1613
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1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1614
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Follow the initial profile and parse/reuse</span></span>
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1615
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1617,8 +1617,8 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1617
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1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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1618
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1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">_Bool</span> <span class="n" style="color: #333;">MultipleLine</span><span class="p">;</span></span>
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1619
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1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">previousSubCommand</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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;">char</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">SUB_COMMAND_MAX_SIZE</span><span class="p">);</span></span>
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1620
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<pre style="margin: 0;">-<span id="LC1620" class="line" lang="c"><span class="idiff left right"> </span></span>
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1621
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<pre style="margin: 0;">-<span id="LC1621" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamIn</span><span class="p">))</span> <span class="p">{</span><span class="idiff left right"> </span></span>
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1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="c"></span>
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1621
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<pre style="margin: 0;">+<span id="LC1621" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamIn</span><span class="p">))</span> <span class="p">{</span></span>
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1622
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetLine</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamIn</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="n" style="color: #333;">PROFILE_MAX_LINE_SIZE</span><span class="p">);</span></span>
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1623
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1623
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<pre style="margin: 0;"> <span id="LC1623" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Line</span><span class="p">;</span></span>
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1624
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1624
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<pre style="margin: 0;"> <span id="LC1624" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1626,12 +1626,12 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1626
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1626
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<pre style="margin: 0;"> <span id="LC1626" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Make a copy */</span></span>
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1627
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1627
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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">currentLineCopy</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1628
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<pre style="margin: 0;"> <span id="LC1628" class="line" lang="c"> <span class="n" style="color: #333;">currentLineCopy</span><span class="p">[</span><span class="n" style="color: #333;">length</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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1629
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<pre style="margin: 0;">-<span id="LC1629" class="line" lang="c"><span class="idiff left right"> </span></span>
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1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="c"></span>
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1630
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1630
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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AnalyzeLine</span><span class="p">(</span><span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">MultipleLine</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1631
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1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Error %i in analysis at line %lu</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">Line</span><span class="p">);</span></span>
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1632
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1632
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<pre style="margin: 0;"> <span id="LC1632" 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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1633
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1633
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="c"> <span class="p">}</span></span>
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1634
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<pre style="margin: 0;">-<span id="LC1634" class="line" lang="c"><span class="idiff left right"> </span></span>
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1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="c"></span>
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1635
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1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Header or matrix */</span></span>
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1636
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1636
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<pre style="margin: 0;"> <span id="LC1636" 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;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">isMatrix</span><span class="p">)</span></span>
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1637
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1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1650,7 +1650,7 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1650
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1650
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="c"> <span class="n" style="color: #333;">CommentStorage</span><span class="p">[</span><span class="n" style="color: #333;">CommentStorageUsed</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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1651
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1651
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="c"> <span class="n" style="color: #333;">CommentStorage</span><span class="p">[</span><span class="n" style="color: #333;">CommentStorageUsed</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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1652
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1652
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="c"> <span class="p">}</span></span>
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1653
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<td class="new_line diff-line-num old" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1653" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'D'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span><span class="idiff left right"> </span></span>
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1653
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<pre style="margin: 0;">+<span id="LC1653" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'D'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'N'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'3'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'D'</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'P'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1685,7 +1685,7 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1685
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1685
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<pre style="margin: 0;"> <span id="LC1685" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrmItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">NNOR</span><span class="p">;</span></span>
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1686
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1686
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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Priority</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrmItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">NNPR</span><span class="p">;</span></span>
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1687
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1687
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrmItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CNTX</span><span class="p">;</span></span>
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1688
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<pre style="margin: 0;">-<span id="LC1688" class="line" lang="c"><span class="idiff left right"> </span></span>
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1688
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="c"></span>
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1689
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1689
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<pre style="margin: 0;"> <span id="LC1689" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"MA /NORMALIZATION: MODE=%i; FUNCTION=%s;"</span><span class="p">,</span> <span class="n" style="color: #333;">Mode</span><span class="p">,</span> <span class="n" style="color: #333;">Function</span><span class="p">);</span></span>
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1690
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1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iCoef</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;">iCoef</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">nCoef</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iCoef</span><span class="p">)</span> <span class="p">{</span></span>
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1691
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1691
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamOut</span><span class="p">,</span> <span class="s" style="color: #d14;">" R%1.1i=%f;"</span><span class="p">,</span> <span class="n" style="color: #333;">iCoef</span><span class="p">,</span> <span class="n" style="color: #333;">nrmItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">RNOP</span><span class="p">[</span><span class="n" style="color: #333;">iCoef</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1707,7 +1707,7 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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1707
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1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">HScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">HCUT</span><span class="p">;</span></span>
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1708
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1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CCUT</span><span class="p">;</span></span>
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1709
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1709
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nModes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutItem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">JCNM</span><span class="p">;</span></span>
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1710
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<pre style="margin: 0;">-<span id="LC1710" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="c"></span>
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1711
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1711
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<pre style="margin: 0;"> <span id="LC1711" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"MA /CUT_OFF: LEVEL=%i; SCORE=%i;"</span><span class="p">,</span> <span class="n" style="color: #333;">Level</span><span class="p">,</span> <span class="n" style="color: #333;">RScore</span><span class="p">);</span></span>
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1712
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1712
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<pre style="margin: 0;"> <span id="LC1712" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">HScore</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1713
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<pre style="margin: 0;"> <span id="LC1713" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamOut</span><span class="p">,</span> <span class="s" style="color: #d14;">" H_SCORE=%u;"</span><span class="p">,</span> <span class="n" style="color: #333;">HScore</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1747,27 +1747,27 @@ int WriteProfile(const char * const restrict FileNameIn, struct Profile * const</td>
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<pre style="margin: 0;"> <span id="LC1747" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1748
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"The following unknown line has been avoided</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">->%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">currentLineCopy</span><span class="p">);</span></span>
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1749
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<pre style="margin: 0;"> <span id="LC1749" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1750" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="c"></span>
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1751
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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1752" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1753" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC1754" class="line" lang="c"> <span class="nl">END_OF_PROFILE:</span></span>
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<pre style="margin: 0;">-<span id="LC1755" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC1757" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Write down the comments now<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Write down the comments now</span></span>
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<pre style="margin: 0;"> <span id="LC1758" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1759
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1759
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<pre style="margin: 0;"> <span id="LC1759" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CommentStorageUsed</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="n" style="color: #333;">CommentStorage</span><span class="p">,</span> <span class="n" style="color: #333;">prfStreamOut</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1760" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="c"></span>
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1761
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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC1762" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Write down the additional comments now<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Write down the additional comments now</span></span>
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<pre style="margin: 0;"> <span id="LC1763" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1764
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1764
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<pre style="margin: 0;"> <span id="LC1764" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">AdditionalComments</span><span class="p">)</span> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="n" style="color: #333;">AdditionalComments</span><span class="p">,</span> <span class="n" style="color: #333;">prfStreamOut</span><span class="p">);</span></span>
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1765
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<pre style="margin: 0;">-<span id="LC1765" class="line" lang="c"><span class="idiff left right"> </span></span>
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1765
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="c"></span>
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1766
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1766
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<pre style="margin: 0;"> <span id="LC1766" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1767
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1767
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<pre style="margin: 0;"> <span id="LC1767" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Terminate profile</span></span>
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1768
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1768
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<pre style="margin: 0;"> <span id="LC1768" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1769
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1769
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<pre style="margin: 0;"> <span id="LC1769" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"//</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">prfStreamOut</span><span class="p">);</span></span>
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1770
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<pre style="margin: 0;">-<span id="LC1770" class="line" lang="c"><span class="idiff left right"> </span></span>
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1770
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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="c"></span>
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1771
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1771
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<pre style="margin: 0;"> <span id="LC1771" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">prfStreamIn</span><span class="p">);</span></span>
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1772
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1772
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<pre style="margin: 0;"> <span id="LC1772" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">CommentStorage</span><span class="p">);</span></span>
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1773
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1773
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<pre style="margin: 0;"> <span id="LC1773" 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="1784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1784,12 +1784,12 @@ void FreeProfile(struct Profile * const prf, const _Bool IsPointer)</td>
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1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="c"> <span class="n" style="color: #333;">_mm_free</span><span class="p">(</span><span class="n" style="color: #333;">nextPrf</span><span class="p">);</span></span>
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1785
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1785
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="c"> <span class="n" style="color: #333;">nextPrf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpPrf</span><span class="p">;</span></span>
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1786
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1786
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<pre style="margin: 0;"> <span id="LC1786" class="line" lang="c"> <span class="p">}</span></span>
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1787
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<pre style="margin: 0;">-<span id="LC1787" class="line" lang="c"><span class="idiff left right"> </span></span>
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1787
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<pre style="margin: 0;">+<span id="LC1787" class="line" lang="c"></span>
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1788
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1788
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<pre style="margin: 0;"> <span id="LC1788" class="line" lang="c"> <span class="n" style="color: #333;">FreeScores</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">prf</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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1789
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1789
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<pre style="margin: 0;"> <span id="LC1789" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Sequence</span><span class="p">);</span></span>
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1790
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1790
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="c"> <span class="n" style="color: #333;">FreeAverage</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Average</span><span class="p">);</span></span>
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1791
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1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Pattern</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Pattern</span><span class="p">);</span></span>
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1792
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<pre style="margin: 0;">-<span id="LC1792" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1792" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IsPointer</span><span class="p">)</span> <span class="p">{</span></span>
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1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="c"> <span class="n" style="color: #333;">_mm_free</span><span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="p">);</span></span>
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1795
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<pre style="margin: 0;"> <span id="LC1795" 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="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1804,9 +1804,9 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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1804
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1804
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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">currentLine</span><span class="p">[</span><span class="n" style="color: #333;">PROFILE_MAX_LINE_SIZE</span><span class="p">]</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">aligned</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)));</span></span>
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<pre style="margin: 0;"> <span id="LC1805" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">ProfileLine</span> <span class="n" style="color: #333;">AnalyzedLine</span><span class="p">;</span></span>
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1806
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<pre style="margin: 0;"> <span id="LC1806" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">_Bool</span> <span class="n" style="color: #333;">MultipleLine</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1807" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1807" class="line" lang="c"></span>
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1808
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<pre style="margin: 0;"> <span id="LC1808" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">Data</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">UniProtMatch</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC1809" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1809" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1810" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1811
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<pre style="margin: 0;"> <span id="LC1811" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Try to open the file, upon failure emmit error</span></span>
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<pre style="margin: 0;"> <span id="LC1812" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1814,8 +1814,8 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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1814
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<pre style="margin: 0;"> <span id="LC1814" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prfStream</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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1815
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<pre style="margin: 0;"> <span id="LC1815" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1817" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC1818" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC1819" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC1820" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Count the number of UniProt statement</span></span>
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<pre style="margin: 0;"> <span id="LC1821" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1824,7 +1824,7 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">FirstAppearanceInFile</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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1825
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<pre style="margin: 0;"> <span id="LC1825" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">StartingLine</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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1826
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1826
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<pre style="margin: 0;"> <span id="LC1826" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1827" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">FilePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1827" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">FilePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1828" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetLine</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="n" style="color: #333;">PROFILE_MAX_LINE_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1829" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1830" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AnalyzeLine</span><span class="p">(</span><span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">MultipleLine</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1846,19 +1846,19 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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<pre style="margin: 0;"> <span id="LC1846" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1847" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Line</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1848" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1849" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1849" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1850" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC1851" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Allocate the memory to hold the data</span></span>
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<pre style="margin: 0;"> <span id="LC1852" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC1853" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">UniqueIdentifier</span><span class="p">)[</span><span class="mi" style="color: #099;">16</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">)[</span><span class="mi" style="color: #099;">16</span><span class="p">])</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">Count</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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1854
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1854
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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EntryName</span><span class="p">)[</span><span class="mi" style="color: #099;">16</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">)[</span><span class="mi" style="color: #099;">16</span><span class="p">])</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">Count</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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1855
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1855
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<pre style="margin: 0;"> <span id="LC1855" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">State</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">Count</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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1856
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<pre style="margin: 0;">-<span id="LC1856" class="line" lang="c"><span class="idiff left right"> </span></span>
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1856
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<pre style="margin: 0;">+<span id="LC1856" class="line" lang="c"></span>
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1857
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1857
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<pre style="margin: 0;"> <span id="LC1857" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UniqueIdentifier</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">EntryName</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">State</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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1858
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1858
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<pre style="margin: 0;"> <span id="LC1858" class="line" lang="c"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1859
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1859
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">FIN</span><span class="p">;</span></span>
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1860
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1860
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<pre style="margin: 0;"> <span id="LC1860" class="line" lang="c"> <span class="p">}</span></span>
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1861
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<pre style="margin: 0;">-<span id="LC1861" class="line" lang="c"><span class="idiff left right"> </span></span>
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1861
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<pre style="margin: 0;">+<span id="LC1861" class="line" lang="c"></span>
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1862
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1862
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<pre style="margin: 0;"> <span id="LC1862" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1863
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1863
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<pre style="margin: 0;"> <span id="LC1863" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Fill in the data</span></span>
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1864
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1864
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<pre style="margin: 0;"> <span id="LC1864" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1874,9 +1874,9 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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1874
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1874
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<pre style="margin: 0;"> <span id="LC1874" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Profile_partial</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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1875
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1875
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<pre style="margin: 0;"> <span id="LC1875" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Profile_false_neg</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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1876
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1876
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<pre style="margin: 0;"> <span id="LC1876" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Profile_false_pos</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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1877
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<pre style="margin: 0;">-<span id="LC1877" class="line" lang="c"><span class="idiff left right"> </span></span>
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1877
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<pre style="margin: 0;">+<span id="LC1877" class="line" lang="c"></span>
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1878
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1878
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<pre style="margin: 0;"> <span id="LC1878" 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;">feof</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1879" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">FilePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span><span class="idiff left right"> </span></span>
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1879
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<pre style="margin: 0;">+<span id="LC1879" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">FilePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span></span>
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1880
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1880
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<pre style="margin: 0;"> <span id="LC1880" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetLine</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">,</span> <span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="n" style="color: #333;">PROFILE_MAX_LINE_SIZE</span><span class="p">);</span></span>
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1881
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1881
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<pre style="margin: 0;"> <span id="LC1881" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1882
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1882
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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AnalyzeLine</span><span class="p">(</span><span class="n" style="color: #333;">currentLine</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">AnalyzedLine</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">MultipleLine</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1915,7 +1915,7 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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1915
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1915
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<pre style="margin: 0;"> <span id="LC1915" class="line" lang="c"> <span class="nl">default:</span></span>
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1916
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1916
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<pre style="margin: 0;"> <span id="LC1916" class="line" lang="c"> <span class="n" style="color: #333;">Profile_unknown</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1917
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1917
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<pre style="margin: 0;"> <span id="LC1917" class="line" lang="c"> <span class="p">}</span></span>
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1918
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<pre style="margin: 0;">-<span id="LC1918" class="line" lang="c"><span class="idiff left right"> </span></span>
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1918
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<pre style="margin: 0;">+<span id="LC1918" class="line" lang="c"></span>
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1919
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1919
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">lCount</span><span class="p">;</span></span>
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1920
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1920
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="c"> <span class="p">}</span></span>
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1921
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1921
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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1927,7 +1927,7 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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1927
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1927
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<pre style="margin: 0;"> <span id="LC1927" class="line" lang="c"> <span class="p">}</span></span>
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1928
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1928
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<pre style="margin: 0;"> <span id="LC1928" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Line</span><span class="p">;</span></span>
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1929
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1929
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<pre style="margin: 0;"> <span id="LC1929" class="line" lang="c"> <span class="p">}</span></span>
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1930
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<pre style="margin: 0;">-<span id="LC1930" class="line" lang="c"><span class="idiff left right"> </span></span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="c"></span>
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1931
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1931
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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1932
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Assign data to structure</span></span>
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1933
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1940,18 +1940,18 @@ int ReadProfileMatch(const char * const restrict FileName, struct UniProtMatch *</td>
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1940
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1940
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<pre style="margin: 0;"> <span id="LC1940" class="line" lang="c"> <span class="n" style="color: #333;">Data</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Partial</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Profile_partial</span><span class="p">;</span></span>
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1941
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1941
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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="c"> <span class="n" style="color: #333;">Data</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">False_negative</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Profile_false_neg</span><span class="p">;</span></span>
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1942
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1942
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<pre style="margin: 0;"> <span id="LC1942" class="line" lang="c"> <span class="n" style="color: #333;">Data</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">False_posistive</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Profile_false_pos</span><span class="p">;</span></span>
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1943
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<pre style="margin: 0;">-<span id="LC1943" class="line" lang="c"><span class="idiff left right"> </span></span>
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1943
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<pre style="margin: 0;">+<span id="LC1943" class="line" lang="c"></span>
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1944
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1944
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<pre style="margin: 0;"> <span id="LC1944" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1945
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<pre style="margin: 0;">-<span id="LC1945" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Close the file<span class="idiff left right"> </span></span></span>
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1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Close the file</span></span>
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1946
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1946
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<pre style="margin: 0;"> <span id="LC1946" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1947
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1947
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<pre style="margin: 0;"> <span id="LC1947" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span></span>
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1948
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1948
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<pre style="margin: 0;"> <span id="LC1948" 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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1949
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<pre style="margin: 0;">-<span id="LC1949" class="line" lang="c"><span class="idiff left right"> </span></span>
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1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="c"></span>
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1950
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<pre style="margin: 0;"> <span id="LC1950" class="line" lang="c"> <span class="nl">FIN1:</span></span>
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1951
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1951
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<pre style="margin: 0;"> <span id="LC1951" class="line" lang="c"> <span class="n" style="color: #333;">FreeProfileMatch</span><span class="p">(</span><span class="n" style="color: #333;">Data</span><span class="p">);</span></span>
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1952
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1952
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<pre style="margin: 0;"> <span id="LC1952" class="line" lang="c"> <span class="nl">FIN:</span></span>
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1953
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1953
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<pre style="margin: 0;"> <span id="LC1953" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">prfStream</span><span class="p">);</span></span>
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1954
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<pre style="margin: 0;">-<span id="LC1954" class="line" lang="c"><span class="idiff left right"> </span></span>
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1954
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<pre style="margin: 0;">+<span id="LC1954" class="line" lang="c"></span>
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1955
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1955
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<pre style="margin: 0;"> <span id="LC1955" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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1956
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1956
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<pre style="margin: 0;"> <span id="LC1956" class="line" lang="c"><span class="p">}</span></span>
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1957
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1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1973,7 +1973,7 @@ void FreeProfileMatch(struct UniProtMatch * Data)</td>
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1973
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1973
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<pre style="margin: 0;"> <span id="LC1973" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "| PFDUMP v" PF_VERSION " |\n"\</span></span>
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1974
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1974
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<pre style="margin: 0;"> <span id="LC1974" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "%----------------------------------------------------------------------------%\n"\</span></span>
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1975
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1975
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<pre style="margin: 0;"> <span id="LC1975" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Built on " __DATE__ " at " __TIME__ ".\n"</span></span>
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1976
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<pre style="margin: 0;">-<span id="LC1976" class="line" lang="c"><span class="idiff left right"> </span></span>
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1976
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<pre style="margin: 0;">+<span id="LC1976" class="line" lang="c"></span>
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1977
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1977
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<pre style="margin: 0;"> <span id="LC1977" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* default value for header is 4 digits*/</span></span>
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1978
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1978
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<pre style="margin: 0;"> <span id="LC1978" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// #define INT_FORMAT "%4i"</span></span>
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1979
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// #define NLOW_FORMAT "NLOW"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1999,13 +1999,13 @@ static unsigned int out_clean = 0;</td>
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1999
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1999
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<pre style="margin: 0;"> <span id="LC1999" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">long_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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2000
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2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="c"><span class="p">{</span></span>
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2001
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2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2002
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<pre style="margin: 0;">-<span id="LC2002" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * These options set a flag.<span class="idiff left right"> </span></span></span>
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2002
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<pre style="margin: 0;">+<span id="LC2002" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * These options set a flag.</span></span>
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2003
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2003
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<pre style="margin: 0;"> <span id="LC2003" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2004
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<pre style="margin: 0;">-<span id="LC2004" class="line" lang="c"><span class="idiff left right"> </span></span>
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2005
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<pre style="margin: 0;">-<span id="LC2005" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*<span class="idiff left right"> </span></span></span>
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2006
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<pre style="margin: 0;">-<span id="LC2006" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * These options don't set a flag. We distinguish them by their indices.<span class="idiff left right"> </span></span></span>
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2004
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<pre style="margin: 0;">+<span id="LC2004" class="line" lang="c"></span>
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2005
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<pre style="margin: 0;">+<span id="LC2005" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2006
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<pre style="margin: 0;">+<span id="LC2006" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * These options don't set a flag. We distinguish them by their indices.</span></span>
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2007
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2007
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<pre style="margin: 0;"> <span id="LC2007" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2008
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<pre style="margin: 0;">-<span id="LC2008" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span><span class="idiff left right"> </span></span>
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2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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2009
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2009
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<pre style="margin: 0;"> <span id="LC2009" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"all"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">},</span></span>
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2010
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2010
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<pre style="margin: 0;"> <span id="LC2010" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"alphabet"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'a'</span><span class="p">},</span></span>
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2011
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2011
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<pre style="margin: 0;"> <span id="LC2011" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"color"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2029,10 +2029,10 @@ static void __attribute__((noreturn)) Usage(FILE * stream)</td>
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2029
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2029
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<pre style="margin: 0;"> <span id="LC2029" class="line" lang="c"> <span class="s" style="color: #d14;">" --color [-c] : output profile reading with colors</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2030
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2030
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<pre style="margin: 0;"> <span id="LC2030" class="line" lang="c"> <span class="s" style="color: #d14;">" --reverse [-r] : reverse profile</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2031
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2031
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<pre style="margin: 0;"> <span id="LC2031" class="line" lang="c"> <span class="s" style="color: #d14;">" --all [-A] : output everything</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2032
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<td class="new_line diff-line-num old" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2032" class="line" lang="c"> <span class="s" style="color: #d14;">" --tables [-T] : output score tables</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="idiff left right"> </span></span>
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2032
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<pre style="margin: 0;">+<span id="LC2032" class="line" lang="c"> <span class="s" style="color: #d14;">" --tables [-T] : output score tables</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2033
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2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="c"> <span class="s" style="color: #d14;">" --alphabet [-a] : output alphabet</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2034
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2034
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="c"> <span class="s" style="color: #d14;">" --profile [-p] : output profile reading</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2035
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<pre style="margin: 0;">-<span id="LC2035" class="line" lang="c"> <span class="s" style="color: #d14;">" --match-table [-m] : output match table</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="idiff left right"> </span></span>
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2035
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<pre style="margin: 0;">+<span id="LC2035" class="line" lang="c"> <span class="s" style="color: #d14;">" --match-table [-m] : output match table</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2036
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2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="c"> <span class="s" style="color: #d14;">" --insertion-table [-i] : output insertion table</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2037
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2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="c"> <span class="s" style="color: #d14;">" --boundary-table [-b] : output boundary table</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2038
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2038
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<pre style="margin: 0;"> <span id="LC2038" class="line" lang="c"> <span class="s" style="color: #d14;">" --transition-table [-t] : output transition table</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2049,7 +2049,7 @@ int main(int argc, char *argv[])</td>
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2049
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2049
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<pre style="margin: 0;"> <span id="LC2049" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">////////////////////////////////////////////////////////////////////////////////////////////////</span></span>
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2050
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2050
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<pre style="margin: 0;"> <span id="LC2050" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// OPTIONS</span></span>
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2051
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2051
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<pre style="margin: 0;"> <span id="LC2051" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">////////////////////////////////////////////////////////////////////////////////////////////////</span></span>
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2052
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<pre style="margin: 0;">-<span id="LC2052" class="line" lang="c"><span class="idiff left right"> </span></span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="c"></span>
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2053
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2053
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<pre style="margin: 0;"> <span id="LC2053" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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2054
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2054
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<pre style="margin: 0;"> <span id="LC2054" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* getopt_long stores the option index here. */</span></span>
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2055
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2055
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<pre style="margin: 0;"> <span id="LC2055" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">option_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2096,24 +2096,24 @@ int main(int argc, char *argv[])</td>
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2096
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2096
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<pre style="margin: 0;"> <span id="LC2096" 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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2097
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2097
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<pre style="margin: 0;"> <span id="LC2097" class="line" lang="c"> <span class="n" style="color: #333;">ProfileFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">];</span></span>
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2098
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2098
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<pre style="margin: 0;"> <span id="LC2098" class="line" lang="c"> <span class="p">}</span></span>
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2099
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<pre style="margin: 0;">-<span id="LC2099" class="line" lang="c"><span class="idiff left right"> </span></span>
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2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="c"></span>
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2100
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2100
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ReadProfile</span><span class="p">(</span><span class="n" style="color: #333;">ProfileFile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2101
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2101
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<pre style="margin: 0;"> <span id="LC2101" class="line" lang="c"> <span class="n" style="color: #333;">FreeProfile</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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2102
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2102
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<pre style="margin: 0;"> <span id="LC2102" 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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2103
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2103
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<pre style="margin: 0;"> <span id="LC2103" class="line" lang="c"> <span class="p">}</span></span>
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2104
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<pre style="margin: 0;">-<span id="LC2104" class="line" lang="c"><span class="idiff left right"> </span></span>
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2104
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<pre style="margin: 0;">+<span id="LC2104" class="line" lang="c"></span>
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2105
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2105
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<pre style="margin: 0;"> <span id="LC2105" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prf</span><span class="p">.</span><span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PF_PATTERN</span><span class="p">)</span> <span class="p">{</span></span>
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2106
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2106
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<pre style="margin: 0;"> <span id="LC2106" class="line" lang="c"> <span class="n" style="color: #333;">FreeProfile</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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2107
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2107
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<pre style="margin: 0;"> <span id="LC2107" 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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2108
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2108
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<pre style="margin: 0;"> <span id="LC2108" class="line" lang="c"> <span class="p">}</span></span>
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2109
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<pre style="margin: 0;">-<span id="LC2109" class="line" lang="c"><span class="idiff left right"> </span></span>
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2109
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<pre style="margin: 0;">+<span id="LC2109" class="line" lang="c"></span>
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2110
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2110
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<pre style="margin: 0;"> <span id="LC2110" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_clean</span><span class="p">)</span> <span class="p">{</span></span>
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2111
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2111
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<pre style="margin: 0;"> <span id="LC2111" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">Footer</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CC Tests output with pfdump</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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2112
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2112
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<pre style="margin: 0;"> <span id="LC2112" class="line" lang="c"> <span class="n" style="color: #333;">WriteProfile</span><span class="p">(</span><span class="n" style="color: #333;">ProfileFile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">,</span> <span class="n" style="color: #333;">Footer</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2113
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2113
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<pre style="margin: 0;"> <span id="LC2113" class="line" lang="c"> <span class="n" style="color: #333;">FreeProfile</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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2114
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2114
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<pre style="margin: 0;"> <span id="LC2114" 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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2115
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2115
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<pre style="margin: 0;"> <span id="LC2115" class="line" lang="c"> <span class="p">}</span></span>
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2116
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<pre style="margin: 0;">-<span id="LC2116" class="line" lang="c"><span class="idiff left right"> </span></span>
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2116
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<pre style="margin: 0;">+<span id="LC2116" class="line" lang="c"></span>
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2117
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2117
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<pre style="margin: 0;"> <span id="LC2117" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isReversed</span><span class="p">)</span> <span class="p">{</span></span>
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2118
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2118
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<pre style="margin: 0;"> <span id="LC2118" class="line" lang="c"> <span class="n" style="color: #333;">rprf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReverseProfile</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">);</span></span>
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2119
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2119
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<pre style="margin: 0;"> <span id="LC2119" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rprf</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error while reversing profile</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>
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<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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_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: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2122,7 +2122,7 @@ int main(int argc, char *argv[])</td>
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2122
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2122
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<pre style="margin: 0;"> <span id="LC2122" class="line" lang="c"> <span class="n" style="color: #333;">pprf</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prf</span><span class="p">;</span></span>
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2123
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2123
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<pre style="margin: 0;"> <span id="LC2123" class="line" lang="c"> <span class="p">}</span></span>
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2124
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2124
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<pre style="margin: 0;"> <span id="LC2124" class="line" lang="c"> <span class="n" style="color: #333;">PrepareExtraTable</span><span class="p">(</span><span class="n" style="color: #333;">pprf</span><span class="p">);</span></span>
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2125
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<pre style="margin: 0;">-<span id="LC2125" class="line" lang="c"><span class="idiff left right"> </span></span>
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2125
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<pre style="margin: 0;">+<span id="LC2125" class="line" lang="c"></span>
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2126
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2126
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<pre style="margin: 0;"> <span id="LC2126" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_alphabet</span><span class="p">)</span> <span class="p">{</span></span>
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2127
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2127
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<pre style="margin: 0;"> <span id="LC2127" class="line" lang="c"> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"Alphabet Mapping"</span><span class="p">);</span></span>
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2128
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2128
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<pre style="margin: 0;"> <span id="LC2128" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ALPHABET_SIZE</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2132,10 +2132,10 @@ int main(int argc, char *argv[])</td>
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2132
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2132
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<pre style="margin: 0;"> <span id="LC2132" class="line" lang="c"> <span class="n" style="color: #333;">puts</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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2133
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2133
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<pre style="margin: 0;"> <span id="LC2133" class="line" lang="c"> <span class="p">}</span></span>
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2134
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2134
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<pre style="margin: 0;"> <span id="LC2134" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">prfLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pprf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2135" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="c"></span>
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2136
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2136
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<pre style="margin: 0;"> <span id="LC2136" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">SMatch</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Match</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pprf</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;">Match</span><span class="p">;</span></span>
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2137
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2137
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<pre style="margin: 0;"> <span id="LC2137" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">SInsertion</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Insertion</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pprf</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;">Insertion</span><span class="p">;</span></span>
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2138
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<pre style="margin: 0;">-<span id="LC2138" class="line" lang="c"><span class="idiff left right"> </span></span>
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2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="c"></span>
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2139
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2139
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<pre style="margin: 0;"> <span id="LC2139" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_match</span><span class="p">)</span> <span class="p">{</span></span>
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2140
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2140
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<pre style="margin: 0;"> <span id="LC2140" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Match matrix with alignment %lu</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">Match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AlignStep</span> <span class="p">);</span></span>
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2141
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2141
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<pre style="margin: 0;"> <span id="LC2141" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" | "</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2148,7 +2148,7 @@ int main(int argc, char *argv[])</td>
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2148
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2148
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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="n" style="color: #333;">LINE</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2149
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2149
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<pre style="margin: 0;"> <span id="LC2149" class="line" lang="c"> <span class="p">}</span></span>
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2150
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2150
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<pre style="margin: 0;"> <span id="LC2150" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2151
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<pre style="margin: 0;">-<span id="LC2151" class="line" lang="c"><span class="idiff left right"> </span></span>
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2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="c"></span>
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2152
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2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">prfLength</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iprf</span><span class="p">)</span> <span class="p">{</span></span>
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2153
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2153
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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">StoredIntegerFormat</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MatchLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Alphabet</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Match</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AlignStep</span><span class="p">];</span></span>
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2154
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2154
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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%3lu | "</span><span class="p">,</span> <span class="n" style="color: #333;">iprf</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2205,11 +2205,11 @@ int main(int argc, char *argv[])</td>
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2205
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2205
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<pre style="margin: 0;"> <span id="LC2205" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2206
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2206
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<pre style="margin: 0;"> <span id="LC2206" class="line" lang="c"> <span class="p">}</span></span>
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2207
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2207
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<pre style="margin: 0;"> <span id="LC2207" class="line" lang="c"> <span class="p">}</span></span>
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2208
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<pre style="margin: 0;">-<span id="LC2208" class="line" lang="c"><span class="idiff left right"> </span></span>
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2208
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<pre style="margin: 0;">+<span id="LC2208" class="line" lang="c"></span>
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2209
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<pre style="margin: 0;"> <span id="LC2209" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_boundaries</span><span class="p">)</span> <span class="p">{</span></span>
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2210
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<pre style="margin: 0;"> <span id="LC2210" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Insertion boundaries matrix with alignment %i</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">INSERTION_BOUNDARIES_SIZE</span> <span class="p">);</span></span>
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2211
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2211
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<pre style="margin: 0;"> <span id="LC2211" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">Header</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_B0"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_B1"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_E0"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_E1"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_BM"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_BI"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_BD"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_BE"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_ME"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_IE"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"_DE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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2212
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<pre style="margin: 0;">-<span id="LC2212" class="line" lang="c"><span class="idiff left right"> </span></span>
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2212
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<pre style="margin: 0;">+<span id="LC2212" class="line" lang="c"></span>
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2213
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2213
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<pre style="margin: 0;"> <span id="LC2213" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="n" style="color: #333;">Header</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2214
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">" |"</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2215
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2215
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<pre style="margin: 0;"> <span id="LC2215" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">strlen</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="mi" style="color: #099;">5</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2232,7 +2232,7 @@ int main(int argc, char *argv[])</td>
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2232
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2232
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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TransitionScores</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">InsertionLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">Transitions</span><span class="p">;</span></span>
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2233
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2233
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<pre style="margin: 0;"> <span id="LC2233" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreTuple</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">FirstSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">FirstSequenceProtein</span><span class="p">;</span></span>
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2234
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2234
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<pre style="margin: 0;"> <span id="LC2234" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ScoreTuple</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span> <span class="kr" style="font-weight: 600;">restrict</span> <span class="n" style="color: #333;">LastSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pprf</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;">Insertion</span><span class="p">.</span><span class="n" style="color: #333;">LastSequenceProtein</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2235" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2235" class="line" lang="c"></span>
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2236
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<pre style="margin: 0;"> <span id="LC2236" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#define PRINT_VALUE(x) { \</span></span>
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2237
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2237
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<pre style="margin: 0;"> <span id="LC2237" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (x == NLOW) {\</span></span>
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2238
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2238
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<pre style="margin: 0;"> <span id="LC2238" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> printf(NLOW_FORMAT " ");\</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2242,7 +2242,7 @@ int main(int argc, char *argv[])</td>
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2242
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2242
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<pre style="margin: 0;"> <span id="LC2242" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> printf(INT_FORMAT " ", x);\</span></span>
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2243
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2243
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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }\</span></span>
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<pre style="margin: 0;"> <span id="LC2244" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC2245" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="c"></span>
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2246
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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Insertion transition matrix with alignment %i</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">INSERTION_TRANSITIONS_SIZE</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">Header2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"MATCH "</span> <span class="n" style="color: #333;">SPACE</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">" "</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">" |"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"INSERTION"</span> <span class="n" style="color: #333;">SPACE</span> <span class="n" style="color: #333;">SPACE</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">" |"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"DELETION "</span> <span class="n" style="color: #333;">SPACE</span> <span class="n" style="color: #333;">SPACE</span> <span class="n" style="color: #333;">SPACE</span>\</span>
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="c"> <span class="s" style="color: #d14;">" |"</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">"EXTRA "</span> <span class="n" style="color: #333;">SPACE</span> <span class="n" style="color: #333;">SPACE</span> <span class="s" style="color: #d14;">" |"</span>\</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2267,39 +2267,39 @@ int main(int argc, char *argv[])</td>
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<pre style="margin: 0;"> <span id="LC2267" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">]);</span></span>
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2268
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2268
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<pre style="margin: 0;"> <span id="LC2268" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]);</span></span>
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2269
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2269
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<pre style="margin: 0;"> <span id="LC2269" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">EXTRA</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC2270" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2270" class="line" lang="c"></span>
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2271
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2271
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<pre style="margin: 0;"> <span id="LC2271" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">]);</span></span>
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2272
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2272
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<pre style="margin: 0;"> <span id="LC2272" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">]);</span></span>
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2273
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2273
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<pre style="margin: 0;"> <span id="LC2273" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]);</span></span>
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2274
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<pre style="margin: 0;"> <span id="LC2274" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">EXTRA</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC2275" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC2276" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC2277" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">]);</span></span>
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2278
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<pre style="margin: 0;"> <span id="LC2278" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]);</span></span>
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2279
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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">EXTRA</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC2280" class="line" lang="c"><span class="idiff left right"> </span></span>
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2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="c"></span>
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2281
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2281
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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">,</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2282
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<pre style="margin: 0;">-<span id="LC2282" class="line" lang="c"><span class="idiff left right"> </span></span>
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2282
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="c"></span>
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2283
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2283
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">EXTRA</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">]);</span></span>
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2284
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2284
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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">EXTRA</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">]);</span></span>
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">InsertionLine</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">EXTRA</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]);</span></span>
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2286
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<pre style="margin: 0;">-<span id="LC2286" class="line" lang="c"><span class="idiff left right"> </span></span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="c"></span>
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2287
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2287
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<pre style="margin: 0;"> <span id="LC2287" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">,</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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2288
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<pre style="margin: 0;">-<span id="LC2288" class="line" lang="c"><span class="idiff left right"> </span></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="c"></span>
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2289
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2289
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<pre style="margin: 0;"> <span id="LC2289" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">LastSeq</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">]);</span></span>
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2290
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2290
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<pre style="margin: 0;"> <span id="LC2290" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">LastSeq</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">]);</span></span>
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2291
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2291
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<pre style="margin: 0;"> <span id="LC2291" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">LastSeq</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">From</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC2292" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="c"></span>
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2293
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<pre style="margin: 0;"> <span id="LC2293" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">,</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2294" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC2295" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">FirstSeq</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">MATCH</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC2296" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">FirstSeq</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">INSERTION</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC2297" class="line" lang="c"> <span class="n" style="color: #333;">PRINT_VALUE</span><span class="p">(</span><span class="n" style="color: #333;">FirstSeq</span><span class="p">[</span><span class="n" style="color: #333;">iprf</span><span class="p">].</span><span class="n" style="color: #333;">To</span><span class="p">[</span><span class="n" style="color: #333;">DELETION</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC2298" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC2299" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2300" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2301" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2302" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2303" class="line" lang="c"> <span class="n" style="color: #333;">FreeProfile</span><span class="p">(</span><span class="n" style="color: #333;">pprf</span><span class="p">,</span> <span class="n" style="color: #333;">isReversed</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2304" 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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<pre style="margin: 0;"> <span id="LC2305" class="line" lang="c"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#7a731b6883e1e46023ef4242a666319467b1ab47"><strong>src/C/utils/system.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -908,7 +908,7 @@ void getSystemInfo(SystemInfo * const info)</td>
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">13</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CPU_Vendor</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Available number of logical processor seen by OS */</span></span>
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="c"> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nOverallCores</span> <span class="o" style="font-weight: 600;">=</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;">int</span><span class="p">)</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_NPROCESSORS_<span class="idiff left">C</span>ON<span class="idiff right">F</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="c"> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nOverallCores</span> <span class="o" style="font-weight: 600;">=</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;">int</span><span class="p">)</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_NPROCESSORS_ON<span class="idiff left right">LN</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">NOBrand</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Not supported by this cpu"</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CPU_Name</span><span class="p">,</span> <span class="n" style="color: #333;">NOBrand</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="c"> </span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#9582d93fae3e6b87bdd789bae160015c4e7e584b"><strong>src/Perl/fasta_to_fastq.pl</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI (csilhah@nus.edu.sg)</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +13,6 @@</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,26 +20,26 @@ open FILE, $file;</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$header</span><span class="p">,</span> <span class="nv" style="color: #008080;">$sequence</span><span class="p">,</span> <span class="nv" style="color: #008080;">$sequence_length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$sequence_quality</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">FILE</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^>(.+)/</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$header</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\@</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$header</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$sequence</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">+</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$sequence_quality</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="perl"> <span class="nv" style="color: #008080;">$header</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence_quality</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^>(.+)/</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$header</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">'')</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\@</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$header</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$sequence</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">+</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$sequence_quality</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"> <span class="p">}</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence</span> <span class="o" style="font-weight: 600;">.=</span> <span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">);</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65</span><span class="p">";</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">//</span><span class="p">,</span> <span class="nv" style="color: #008080;">$qual</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$sequence_length</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">$sequence_quality</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$qual</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$qual</span><span class="p">)]}</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"> <span class="nv" style="color: #008080;">$header</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'';</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'';</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence_quality</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'';</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence</span> <span class="o" style="font-weight: 600;">.=</span> <span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">//</span><span class="p">,</span> <span class="nv" style="color: #008080;">$qual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$sequence_length</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">$sequence_quality</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$qual</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$qual</span><span class="p">)]}</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: #008080;">FILE</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\@</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$header</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: #008080;">Std</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#a90d30287a920b2225b061ac70a46ee73c5957b1"><strong>src/Perl/scramble_fasta.pl</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ usage:</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"><span class="s1" style="color: #d14;"> scramble_fasta.pl [options] fasta-file...</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="perl"><span class="s1" style="color: #d14;">This script produces"random" or "shuffled" sequences according to a</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="s1" style="color: #d14;">This script produces<span class="idiff left right"> </span>"random" or "shuffled" sequences according to a</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="s1" style="color: #d14;">model and to a set of parameters. All sequences are read and written</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"><span class="s1" style="color: #d14;">in FASTA format. No distinction is made between DNA and protein</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="s1" style="color: #d14;">sequences. All letter are converted to uppercase. Gaps are</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: #008080;">Std</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#edc76d1689c1a7f0bd0401f05fd6b05ea7f6e15b"><strong>tests/examples/test_V3.sh.cmake</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,9 +19,9 @@ PFW=$<TARGET_FILE:pfw></td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cmake">PTOH=$<TARGET_FILE:ptoh></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cmake">PTOF=$<TARGET_FILE:ptof></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cmake">P2FT=$<TARGET_FILE:2ft> <span class="c1" style="color: #998; font-style: italic;"># NB: sh does not allow variable name starting with a digit</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cmake"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cmake">SORT_PSA=@PERL_SCRIPT_DIR@/sort_fasta.pl <span class="c1" style="color: #998; font-style: italic;"># FIXME: use cmake syntax<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cmake">MAKE_IUPAC_CMP=@PERL_SCRIPT_DIR@/make_iupac_cmp.pl <span class="c1" style="color: #998; font-style: italic;"># FIXME: use cmake syntax<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake">SORT_PSA=@PERL_SCRIPT_DIR@/sort_fasta.pl <span class="c1" style="color: #998; font-style: italic;"># FIXME: use cmake syntax</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake">MAKE_IUPAC_CMP=@PERL_SCRIPT_DIR@/make_iupac_cmp.pl <span class="c1" style="color: #998; font-style: italic;"># FIXME: use cmake syntax</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cmake">SCRAMBLE=@PERL_SCRIPT_DIR@/scramble_fasta.pl <span class="c1" style="color: #998; font-style: italic;"># FIXME: use cmake syntax</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cmake">CMPDIR=@DATA_DIR@/Matrices</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,15 +29,15 @@ TMPDIR=/tmp/test_V3</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cmake">mkdir -p $TMPDIR</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The PFTOOLS is a powerful software to align biological sequences.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Owing to the 'generalized profile syntax', it allows the fine-tuning<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># of an alignent scoring system, beyond what is feasible by most other<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># software. Despite the PFTOOLS are crippled by a lot of legacy code,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># they are still extremely useful for precision work<span class="idiff left right"> . </span></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The PFTOOLS is a powerful software to align biological sequences.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Owing to the 'generalized profile syntax', it allows the fine-tuning</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># of an alignent scoring system, beyond what is feasible by most other</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># software. Despite the PFTOOLS are crippled by a lot of legacy code,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># they are still extremely useful for precision work<span class="idiff left right">.</span></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Nota bene to use this script as a testsuite:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># (1) The output order of pfsearch is reproducible, as well as the one of<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># pfsearchV3 with -t 1.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># (1) The output order of pfsearch is reproducible, as well as the one of</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># pfsearchV3 with -t 1.</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># (2) Refrain using any pipe.</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cmake"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ mkdir -p $TMPDIR</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Searching for the occurence of the SH3 domain within the VAV oncogene,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># using pfsearch V2 ...</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cmake">$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cmake">$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># ...and using pfsearch V3:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,8 +53,8 @@ $PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cmake">$PFSEARCHV3 -n -t 1 -f ./sh3.prf ./VAV_HUMAN.seq</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Create a database of sequences and a database of profiles, each one<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># with two entries.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Create a database of sequences and a database of profiles, each one</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># with two entries.</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cmake">cat ./VAV_HUMAN.seq ./VAV_RAT.seq > $TMPDIR/VAV.seq</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cmake">cat ./sh2.prf ./sh3.prf > $TMPDIR/SHX.prf</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,10 +79,10 @@ $PFSEARCHV3 -f -n -t 2 -o 6 ./sh3.prf -f $TMPDIR/VAV.seq >> $TMPDIR/SHX.pfsearch</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cmake">$PFSCANV3 -f -n -o 6 $TMPDIR/SHX.prf $TMPDIR/VAV.seq > $TMPDIR/SHX.pfscan3.hit</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># All these commands produces exactly the same list of matched<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># sequences, with the same raw scores and coordinates.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># All these commands produces exactly the same list of matched</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># sequences, with the same raw scores and coordinates.</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># However the output order is not necessarily preserved here.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># However the output order is not necessarily preserved here.</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Let's verify that the output are comparable after fixing FASTA headers</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,7 +95,7 @@ diff $TMPDIR/SHX.pfscan2.out $TMPDIR/SHX.pfsearch2.out # expecting no differenc</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cmake">diff $TMPDIR/SHX.pfscan2.out $TMPDIR/SHX.pfsearch3.out <span class="c1" style="color: #998; font-style: italic;"># expecting no difference</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Pfsearch/pfscan V2 supports the following input formats for sequence:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Pfsearch/pfscan V2 supports the following input formats for sequence:</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># FASTA, Swiss-Prot and EMBL.</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cmake">$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq <span class="c1" style="color: #998; font-style: italic;"># FASTA</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,10 +105,10 @@ $PFSEARCH ./sh3.prf ./GTPA_HUMAN.dat # SwissProt</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cmake">$PFSCAN ./GTPA_HUMAN.dat ./sh3.prf <span class="c1" style="color: #998; font-style: italic;"># SwissProt</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cmake">$PFSEARCH ./ecp.prf ./CVPBR322.embl <span class="c1" style="color: #998; font-style: italic;"># EMBL</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cmake">$PFSCAN ./CVPBR322.embl ./ecp.prf <span class="c1" style="color: #998; font-style: italic;"># EMBL<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cmake">$PFSCAN ./CVPBR322.embl ./ecp.prf <span class="c1" style="color: #998; font-style: italic;"># EMBL</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Pfsearch/pfscan V3 supports the following input formats for sequence:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Pfsearch/pfscan V3 supports the following input formats for sequence:</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># FASTA and FASTQ.</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cmake">$PFSEARCHV3 -n -t 1 -f ./sh3.prf ./VAV_HUMAN.seq <span class="c1" style="color: #998; font-style: italic;"># FASTA</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,7 +117,7 @@ cat ./CVPBR322.embl \</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cmake">| perl -ne '<span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>/^ID +<span class="p">(</span>\w+<span class="p">)</span>/<span class="p">)</span>{print <span class="s2" style="color: #d14;">">$1</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span>}<span class="nf" style="color: #900; font-weight: 600;">elsif</span><span class="p">(</span>/^ /<span class="p">)</span>{s/[\s\d]+//g;print <span class="s2" style="color: #d14;">"$_</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span>;}' \</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cmake">> $TMPDIR/CVPBR322.fa <span class="c1" style="color: #998; font-style: italic;"># Extract FASTA from EMBL</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cmake">$PFSEARCHV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa</span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cmake">$PFSCANV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cmake">$PFSCANV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cmake">$PFSEARCHV3 -n -t 1 -q ./hiv.prf ./hiv.fastq <span class="c1" style="color: #998; font-style: italic;"># FASTQ</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cmake">$PFSCANV3 -n -t 1 -q ./hiv.prf ./hiv.fastq <span class="c1" style="color: #998; font-style: italic;"># FASTQ</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,8 +136,8 @@ $PFSEARCHV3 -n -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR3</td>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cmake">diff -b $TMPDIR/ecp.CVPBR322.2.hit $TMPDIR/ecp.CVPBR322.3.hit <span class="c1" style="color: #998; font-style: italic;"># expecting no difference</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The different PSA (i.e FASTA) output formats differ by the content<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># their headers. The usage of XPSA (-o 6) is strongly recommended, the<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The different PSA (i.e FASTA) output formats differ by the content</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># their headers. The usage of XPSA (-o 6) is strongly recommended, the</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># other formats being preserved for legacy.</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cmake">$PFSEARCHV3 -n -f -o 1 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA -</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -147,10 +147,10 @@ $PFSEARCHV3 -n -f -o 4 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA -</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cmake">$PFSEARCHV3 -n -f -o 6 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA - <span class="c1" style="color: #998; font-style: italic;"># recommended</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Multiple sequence alignment (MSA) can easily be produced from PSA<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Multiple sequence alignment (MSA) can easily be produced from PSA</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># using psa2msa (V2)</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cmake">$PFSEARCHV3 -n -f -o 6 ./ecp.prf $TMPDIR/CVPBR322.fa | $SORT_PSA - | $PSA2MSA<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cmake">$PFSEARCHV3 -n -f -o 6 ./ecp.prf $TMPDIR/CVPBR322.fa | $SORT_PSA - | $PSA2MSA</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># V3 has two new output formats: TSV and SAM</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -169,15 +169,15 @@ $PFSEARCHV3 -n -t 1 -q -o 8 ./hiv.prf ./hiv.fastq # FASTQ to SAM</td>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cmake">$PFSEARCHV3 -n -t 1 -q -b -o 8 ./hiv.prf ./hiv.fastq <span class="c1" style="color: #998; font-style: italic;"># FASTQ to SAM</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cmake"></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Index can optionaly be used to speed-up database upload for pfsearch.<span class="idiff left right"> </span></span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># This should be especially usefull for repetitive database searches<span class="idiff left right"> </span></span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># using the heuristic.<span class="idiff left right"> </span></span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Index can optionaly be used to speed-up database upload for pfsearch.</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># This should be especially usefull for repetitive database searches</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># using the heuristic.</span></span>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cmake"></span>
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cmake">$PFINDEX -f -o $TMPDIR/CVPBR322.fa.idx $TMPDIR/CVPBR322.fa</span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cmake">$PFSEARCHV3 -n -f -o 7 ./ecp.prf $TMPDIR/CVPBR322.fa | sort > $TMPDIR/A.out <span class="c1" style="color: #998; font-style: italic;"># FASTA to TSV</span></span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cmake">$PFSEARCHV3 -n -f -i $TMPDIR/CVPBR322.fa.idx -o 7 ./ecp.prf $TMPDIR/CVPBR322.fa | sort > $TMPDIR/B.out <span class="c1" style="color: #998; font-style: italic;"># FASTA to TSV</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cmake">diff $TMPDIR/A.out $TMPDIR/B.out<span class="idiff left right"> </span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cmake">diff $TMPDIR/A.out $TMPDIR/B.out</span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cmake"></span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cmake">$PFINDEX -q -o $TMPDIR/hiv.fastq.idx ./hiv.fastq</span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cmake">$PFSEARCHV3 -n -q -b -o 8 ./hiv.prf ./hiv.fastq | sort > $TMPDIR/A.out</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -185,23 +185,23 @@ $PFSEARCHV3 -n -q -b -o 8 -i $TMPDIR/hiv.fastq.idx ./hiv.prf ./hiv.fastq | sort</td>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cmake">diff $TMPDIR/A.out $TMPDIR/B.out</span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cmake"></span>
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Profile and/or sequence can be reversed on the fly. If both are<span class="idiff left right"> </span></span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Profile and/or sequence can be reversed on the fly. If both are</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># reversed the match score is the same</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cmake">$PFSEARCHV3 -f -a rand_dna.prf rand_dna.seq</span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cmake">$PFSEARCHV3 -f -a -r -R rand_dna.prf rand_dna.seq</span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># There is a much better support of rev/comp search in DNA sequences,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># There is a much better support of rev/comp search in DNA sequences,</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># featuring the full IUPAC code.</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># To illustrate these capabilities, let build a profile for bacterial</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># 16S sequence, starting from the Rfam seed RF00177.msa. First create<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># 16S sequence, starting from the Rfam seed RF00177.msa. First create</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># an adhoc substitution matrix</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cmake">$MAKE_IUPAC_CMP -M 20 -m -30 > $TMPDIR/iupac20-30.cmp</span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># ... let build a profile for bacterial 16S sequence, starting from<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># ... let build a profile for bacterial 16S sequence, starting from</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># the Rfam seed RF00177.msa.</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cmake">cat ./RF00177.msa \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,7 +224,7 @@ cat ./SRR9619541.sample.fastq \</td>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cmake">> $TMPDIR/permut.fa</span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># $PFCALIBRATEV3 -F $TMPDIR/permut.fa $TMPDIR/16S.prf.tmp > $TMPDIR/16S.prf</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># $PFSEARCHV3 -t 1 -n -q $TMPDIR/16S.prf $TMPDIR/small.sample.fastq<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># $PFSEARCHV3 -t 1 -n -q $TMPDIR/16S.prf $TMPDIR/small.sample.fastq</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#----------------------------------------------------------------------#</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Verify handling of characters not in the profile alphabet</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -240,7 +240,7 @@ ACGTWACGT</td>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cmake">EOI</span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cmake">$PFMAKE -m -3 -S 0.01 -F 100 $TMPDIR/ACGTAACGT.seq $CMPDIR/dna_50_40.cmp > $TMPDIR/ACGTAACGT.prf</span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cmake">$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTAACGT.seq <span class="c1" style="color: #998; font-style: italic;"># raw_score=450 PSA=ACGTAACGT<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cmake">$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTAACGT.seq <span class="c1" style="color: #998; font-style: italic;"># raw_score=450 PSA=ACGTAACGT</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cmake">$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTWACGT.seq <span class="c1" style="color: #998; font-style: italic;"># raw_score=383 PSA=ACGTWACGT (not ACGTXACGT)</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cmake"></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#25ebe0897656d14d609c490fa9e73f26e61ed9f0"><strong>tests/examples/test_V3_output.sh.cmake</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,3 @@ mkdir -p $TMPDIR</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake">sh -ve ./test_V3.sh > $TMPDIR/test_V3.out 2>/dev/null</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake">diff ./test_V3.out $TMPDIR/test_V3.out</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"></span></pre>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cmake"></span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#0130171c343ee37c2f9a892a3094cf0a7c3a3d01"><strong>tests/examples/test_pfsearchV3_iupac.pl.cmake</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">use strict;</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/b51b2b7349627b2841d5d88e473a859b292d2696#e49e80e7fdd233ba13714866dbec311e937d3a73"><strong>tests/examples/test_scan_search.pl.cmake</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">use strict;</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
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