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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/stacks">Debian Med / stacks</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/1cf0136236c1e05d11b41a19d4df06485c930c2e">1cf01362</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-09-15T03:15:53+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.54+dfsg</pre>
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<h4>4 changed files:</h4>
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<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<a href="#0c4ded025684d2dd954d9125d5b5a1e62f34a876">
scripts/stacks-integrate-alignments
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<a href="#55886629c6dcee7a5c2a0a0b4f3966e6939cccb4">
src/renz.cc
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/1cf0136236c1e05d11b41a19d4df06485c930c2e#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Stacks</span> <span class="m" style="color: #099;">2.54</span> <span class="p">-</span> <span class="n" style="color: #333;">September</span> <span class="m" style="color: #099;">03</span><span class="p">,</span> <span class="m" style="color: #099;">2020</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p">--------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="n" style="color: #333;">Feature</span><span class="p">:</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">BtgI</span><span class="p">,</span> <span class="n" style="color: #333;">PacI</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">PspXI</span><span class="p">,</span> <span class="n" style="color: #333;">HpyCH4IV</span> <span class="n" style="color: #333;">restriction</span> <span class="n" style="color: #333;">enzymes</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">process_radtags</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="n" style="color: #333;">Bugfix</span><span class="p">:</span> <span class="n" style="color: #333;">stacks</span><span class="p">-</span><span class="n" style="color: #333;">integrate</span><span class="p">-</span><span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">tab</span> <span class="n" style="color: #333;">characters</span> <span class="n" style="color: #333;">fed</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">grep</span> <span class="n" style="color: #333;">were</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">being</span> <span class="n" style="color: #333;">interpreted</span> <span class="n" style="color: #333;">properly</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Stacks</span> <span class="m" style="color: #099;">2.53</span> <span class="p">-</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">28</span><span class="p">,</span> <span class="m" style="color: #099;">2020</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"><span class="p">----------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">Bugfix</span><span class="p">:</span> <span class="n" style="color: #333;">denovo_map</span><span class="p">.</span><span class="n" style="color: #333;">pl</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">cstacks</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">non</span><span class="p">-</span><span class="n" style="color: #333;">genetic</span> <span class="n" style="color: #333;">map</span> <span class="n" style="color: #333;">datasets</span><span class="p">.</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/1cf0136236c1e05d11b41a19d4df06485c930c2e#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</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">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ(2.59)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.5<span class="idiff left right">3</span>])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.5<span class="idiff left right">4</span>])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AC_CONFIG_AUX_DIR([config])</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_SRCDIR([src/ustacks.cc])</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/1cf0136236c1e05d11b41a19d4df06485c930c2e#0c4ded025684d2dd954d9125d5b5a1e62f34a876"><strong>scripts/stacks-integrate-alignments</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">@@ -116,7 +116,7 @@ samtools view -F 0x904 "$bam_f" |</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">join</span> <span class="nt" style="color: #000080;">-t</span> <span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\t</span><span class="s1" style="color: #d14;">'</span> <span class="nt" style="color: #000080;">-12</span> <span class="nt" style="color: #000080;">-22</span> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"1.1 1.2 2.1 1.3 1.4"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"> - <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="shell"> <<span class="o" style="font-weight: 600;">(</span>samtools view <span class="nt" style="color: #000080;">-H</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$bam_f</span><span class="s2" style="color: #d14;">"</span> |</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'^@SQ'</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-oE</span> <span class="s1" style="color: #d14;">'SN:[^\t]+'</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-c4-</span> |</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'^@SQ'</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-oE</span> <span class="s1" style="color: #d14;"><span class="idiff left right">$</span>'SN:[^</span><span class="se" style="color: #d14;">\t</span><span class="s1" style="color: #d14;">]+'</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-c4-</span> |</span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{printf NR"\t"$1"\n"}'</span> |</span>
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: #000080;">-k2</span>,2</span>
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122
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="shell"> <span class="o" style="font-weight: 600;">)</span> |</span>
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<li id="55886629c6dcee7a5c2a0a0b4f3966e6939cccb4">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/1cf0136236c1e05d11b41a19d4df06485c930c2e#55886629c6dcee7a5c2a0a0b4f3966e6939cccb4"><strong>src/renz.cc</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,6 +36,8 @@ const char *bspDI[] = {"CGAT", // AT/CGAT, BspDI</td>
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATCG"</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="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bstYI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"GATCC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GATCT"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// R/GATCY, BstYI (also known as PsuI)</span></span>
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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GGATC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AGATC"</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">btgI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"CACGG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CGCGG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CATGG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CGTGG"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// C/CRYGG, BtgI</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="s" style="color: #d14;">"CCGTG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCGCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCATG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCACG"</span><span class="p">};</span></span>
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39
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cac8I</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"AGC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CGC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GGC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TGC"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// GCN/NGC, Cac8I</span></span>
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40
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GCT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GCC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GCA"</span><span class="p">};</span></span>
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41
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">claI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"CGAT"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// AT/CGAT, ClaI</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +64,8 @@ const char *hindIII[] = {"AGCTT", // A/AGCTT, HindIII</td>
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62
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="s" style="color: #d14;">"TCGAA"</span><span class="p">};</span></span>
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63
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hpaII</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"CGG"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// C/CGG, HpaII</span></span>
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64
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="s" style="color: #d14;">"CCG"</span><span class="p">};</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="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;">hpyCH4IV</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"CGT"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// A/CGT, HpyCH4IV</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ACG"</span><span class="p">};</span></span>
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65
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kpnI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"GTACC"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// C/CATGG, KpnI</span></span>
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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
66
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GGTAC"</span><span class="p">};</span></span>
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67
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mluCI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"AATT"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// AATT, MluCI</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(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="102" style="width: 35px; color: rgba(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">@@ -98,6 +102,10 @@ const char *nsiI[] = {"TGCAT", // ATGCA/T, NsiI</td>
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98
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ATGCA"</span><span class="p">};</span></span>
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99
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nspI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"CATGA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CATGG"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// R/CATGY, NspI</span></span>
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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GCATG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACATG"</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pacI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"ATTAA"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// AAT/TAATT, PacI</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="s" style="color: #d14;">"TTAAT"</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pspXI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"TCGAGC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TCGAGG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TCGAGT"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// VC/TCGAGB, PspXI</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="s" style="color: #d14;">"GCTCGA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCTCGA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACTCGA"</span><span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pstI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"TGCAG"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// CTGCA/G, PstI</span></span>
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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="s" style="color: #d14;">"CTGCA"</span><span class="p">};</span></span>
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103
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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rsaI</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"AC"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// GT/AC, RsaI</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(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="186" style="width: 35px; color: rgba(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">@@ -178,6 +186,10 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma</td>
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178
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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"apaLI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">apaLI</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// G/TGCAC, ApaLI</span></span>
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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
179
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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"hinP1I"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hinP1I</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// G/CGC, HinP1I</span></span>
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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
180
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"bbvCI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bbvCI</span><span class="p">;</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"btgI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">btgI</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// C/CRYGG, BtgI</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"pacI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pacI</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// AAT/TAATT, PacI</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"pspXI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pspXI</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// VC/TCGAGB, PspXI</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">renz</span><span class="p">[</span><span class="s" style="color: #d14;">"hpyCH4IV"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hpyCH4IV</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// A/CGT, HpyCH4IV</span></span>
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181
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"></span>
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182
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"sbfI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"pstI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="231" style="width: 35px; color: rgba(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="243" style="width: 35px; color: rgba(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">@@ -231,7 +243,11 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma</td>
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231
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"apaLI"</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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232
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"hinP1I"</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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233
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"bbvCI"</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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234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"btgI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"pacI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"pspXI"</span><span class="p">]</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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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_cnt</span><span class="p">[</span><span class="s" style="color: #d14;">"hpyCH4IV"</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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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> </span>
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235
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<td class="diff-line-num new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"sbfI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
236
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<td class="diff-line-num new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"pstI"</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>
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<td class="diff-line-num old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
237
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<td class="diff-line-num new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"notI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</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">@@ -284,6 +300,10 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma</td>
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284
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"apaLI"</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>
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285
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"hinP1I"</span><span class="p">]</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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<td class="diff-line-num old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
286
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"bbvCI"</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>
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<td class="diff-line-num new old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"btgI"</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>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"pacI"</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>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"pspXI"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">renz_len</span><span class="p">[</span><span class="s" style="color: #d14;">"hpyCH4IV"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="288" style="width: 35px; color: rgba(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="LC308" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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