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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/baitfisher">Debian Med / baitfisher</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70">aea05c6b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-17T19:53:06+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.7+git20190123.241d060+dfsg</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a74d2945c6a02a0d33c20eeb36b64f5df315f34f">
CBlastParser.h
</a>
</li>
<li class="file-stats">
<a href="#0f42436734a2b866d857a984331613dcc9443bff">
Documentation/BaitFisher-BaitFilter-Manual.tex
</a>
</li>
<li class="file-stats">
<a href="#0a487eb3619e324c66ce565fab0e7e223dcb120f">
global-types-and-parameters.cpp
</a>
</li>
<li class="file-stats">
<a href="#99f55a6afdb0693b93a8b6b7bdfffc63f7f38848">
range_functions.h
</a>
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</ul>
<h4>Changes:</h4>
<li id="a74d2945c6a02a0d33c20eeb36b64f5df315f34f">
<a href="https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70#a74d2945c6a02a0d33c20eeb36b64f5df315f34f"><strong>CBlastParser.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="575" 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">@@ -575,7 +575,7 @@ class CBlast_parser</td>
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575
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">removeSpacesFront</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="576" 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">
576
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<td class="diff-line-num new_line" data-linenumber="576" 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">
576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">removeSpacesBack</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="577" 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">
577
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<td class="diff-line-num new_line" data-linenumber="577" 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">
577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="578" 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">
578
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<td class="diff-line-num new_line old" data-linenumber="578" 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="LC578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</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 class="c1" style="color: #998; font-style: italic;">// if not a comment - allows to read the -m 9 in addition to the -m 8 output format</span></span>
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<td class="diff-line-num new new_line" data-linenumber="578" 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">
578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</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 class="c1" style="color: #998; font-style: italic;">// if not a comment - allows <span class="idiff left right">us </span>to read the -m 9 in addition to the -m 8 output format</span></span>
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579
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="n" style="color: #333;">CBlastHit</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CBlastHit</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">counter</span><span class="p">);</span></span>
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581
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cpp"></span>
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<li id="0f42436734a2b866d857a984331613dcc9443bff">
<a href="https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70#0f42436734a2b866d857a984331613dcc9443bff"><strong>Documentation/BaitFisher-BaitFilter-Manual.tex</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 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">@@ -1515,7 +1515,7 @@ number of baits as the optimality criterion. As above, the</td>
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="tex">console-output is redirected to two files.</span>
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="tex"></span>
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span> With BaitFilter version 1.0.6 a new filter mode has been introduced.</span>
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<pre style="margin: 0;">-<span id="LC1518" class="line" lang="tex">This mode allows to keep not only one but multiple bait regions per feature, or alignment, if the</span>
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="tex">This mode allows <span class="idiff left right">you </span>to keep not only one but multiple bait regions per feature, or alignment, if the</span>
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<pre style="margin: 0;"> <span id="LC1519" class="line" lang="tex">length of the feature or alignment is long enough so that two or more bait regions can be situated</span>
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<pre style="margin: 0;"> <span id="LC1520" class="line" lang="tex">in the alignment with a minimum distance.</span>
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="tex"></span>
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<li id="0a487eb3619e324c66ce565fab0e7e223dcb120f">
<a href="https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70#0a487eb3619e324c66ce565fab0e7e223dcb120f"><strong>global-types-and-parameters.cpp</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">@@ -237,7 +237,7 @@ void read_and_init_parameters(int argc, char** argv, ostream &logerr)</td>
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">ValueArg</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">blast_extra_commandline_Arg</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"blast-extra-commandline"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="s" style="color: #d14;">"When invoking the blast command, extra command line parameters can be passed to the blast program with the aid of this option. As an example, "</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="s" style="color: #d14;">"this option allows to specify the number of threads the blast program should use. Example: --blast-extra-commandline </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-num_threads 20</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> sets the number of threads to 20. "</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="s" style="color: #d14;">"this option allows <span class="idiff left right">you </span>to specify the number of threads the blast program should use. Example: --blast-extra-commandline </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-num_threads 20</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> sets the number of threads to 20. "</span><span class="p">,</span></span>
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"string"</span><span class="p">);</span></span>
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242
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span> <span class="n" style="color: #333;">blast_extra_commandline_Arg</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -637,7 +637,7 @@ void print_parameters(FILE *of, const char *s)</td>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"> <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;">global_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">of</span><span class="p">,</span> <span class="s" style="color: #d14;">"%sFilter mode: Blast filter: Remove all bait regions from output that belong to the FEATUE in which one bait has at least two good hits to the reference genome.</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;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">of</span><span class="p">,</span> <span class="s" style="color: #d14;">"%sFilter mode: Blast filter: Remove all bait regions from output that belong to the FEATU<span class="idiff left right">R</span>E in which one bait has at least two good hits to the reference genome.</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;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="cpp"> <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;">global_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="cpp"> <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">@@ -765,7 +765,7 @@ void print_parameters(ostream &os, const char *s)</td>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"> <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;">global_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</span><span class="p">)</span></span>
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Filter mode: Blast filter: Remove all bait regions from output that belong to the FEATUE in which one bait has at least two good hits to the reference genome.</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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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Filter mode: Blast filter: Remove all bait regions from output that belong to the FEATU<span class="idiff left right">R</span>E in which one bait has at least two good hits to the reference genome.</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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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="p">}</span></span>
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <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;">global_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'x'</span><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="cpp"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70#99f55a6afdb0693b93a8b6b7bdfffc63f7f38848"><strong>range_functions.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -921,7 +921,7 @@ class CRangeList</td>
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// coverage_len allows to specify a range - double check that feature.</span></span>
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// coverage_len allows <span class="idiff left right">us </span>to specify a range - double check that feature.</span></span>
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">coverage_rel</span><span class="p">(</span><span class="n" style="color: #333;">Crange</span> <span class="n" style="color: #333;">bds</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;">CRangeList</span> <span class="n" style="color: #333;">rl_tmp</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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