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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/paraclu">Debian Med / paraclu</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/paraclu/-/commit/a3528ceabfcc774bbf3099a9e4375126204cb241">a3528cea</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-06-05T01:27:25+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10</pre>
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<h4>4 changed files:</h4>
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<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
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−
ChangeLog.txt
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#fda3484edf8db0684440157ce0b110d784d42704">
README.txt
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+
paraclu_sketch.png
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/paraclu/-/commit/a3528ceabfcc774bbf3099a9e4375126204cb241#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2012-12-14 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * README.txt, paraclu-cut.sh:</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> ! New version of paraclu-cut: use its -s option to get the old</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> behaviour</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [c1086ad752b4] [tip]</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">2012-09-03 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> * README.txt:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Clarified the minValue parameter in the README</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> [77214c740db7]</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">2012-08-09 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> * README.txt:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Made the README convertible to a manpage by pandoc (thanks: Charles</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> Plessy)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> [27f84a76abc0]</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">2012-08-08 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> * Makefile:</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> Generalized the Makefile a bit</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> [77cfa417a78a]</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">2011-11-02 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> * Makefile:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> Made the Makefile more flexible (thanks: Charles Plessy)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> [4e9b8fb9d6b0]</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">2011-08-16 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> * README.txt, paraclu.cc:</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> Try to make the C++ strictly correct and portable</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> [cf2ffcee14a7]</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> * ctss-merge.sh:</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> Removed a too-specialized script</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> [efcdfe3977b0]</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> * COPYING.txt, Makefile, README.txt, paraclu-cut.sh:</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> Modified the package for public distribution</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> [1d012dc9bd10]</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">2011-02-08 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> * README.txt:</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> Simplified the README</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> [4f75340f8a78]</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> * Makefile, README.txt, ctss-merge.sh, paraclu-cut.sh, paraclu.cc:</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> Start using version control</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> [55b4fd7f6316]</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/paraclu/-/commit/a3528ceabfcc774bbf3099a9e4375126204cb241#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXX</span> <span class="o" style="font-weight: 600;">=</span> g++</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-W</span> <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">paraclu</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nl">paraclu</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">paraclu.cc Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nv" style="color: #008080;">$(CPPFLAGS)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> paraclu.cc</span>
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8
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span><span class="idiff left"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">FORCE</span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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10
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> paraclu</span>
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11
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nl">log</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">FORCE</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"> hg log <span class="nt" style="color: #000080;">--style</span> changelog <span class="o" style="font-weight: 600;">></span> ChangeLog.txt</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"><span class="nv" style="color: #008080;">distdir</span> <span class="o" style="font-weight: 600;">=</span> paraclu-<span class="sb" style="color: #d14;">`</span>hg <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-n</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"><span class="nl">dist</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">log</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">${distdir}</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">*</span>.cc <span class="k" style="font-weight: 600;">*</span>.sh <span class="k" style="font-weight: 600;">*</span>.txt Makefile <span class="nv" style="color: #008080;">${distdir}</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"> zip <span class="nt" style="color: #000080;">-qrm</span> <span class="nv" style="color: #008080;">${distdir}</span> <span class="nv" style="color: #008080;">${distdir}</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="nl">FORCE</span><span class="o" style="font-weight: 600;">:</span></span></pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nl">tag</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"> git tag <span class="nt" style="color: #000080;">-m</span> <span class="s2" style="color: #d14;">""</span> <span class="sb" style="color: #d14;">`</span>git rev-list HEAD^ | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-c</span> .<span class="sb" style="color: #d14;">`</span></span></pre>
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<a href="https://salsa.debian.org/med-team/paraclu/-/commit/a3528ceabfcc774bbf3099a9e4375126204cb241#fda3484edf8db0684440157ce0b110d784d42704"><strong>README.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" 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="137" 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">@@ -137,9 +137,3 @@ If you use paraclu in your research, please cite:</td>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">"A code for transcription initiation in mammalian genomes"</span>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">MC Frith, E Valen, A Krogh, Y Hayashizaki, P Carninci, A Sandelin</span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">Genome Research 2008 18(1):1-12.</span></pre>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext">CONTACT</span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">Website: http://www.cbrc.jp/paraclu/</span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">E-mail: paraclu (ATmark) cbrc (dot) jp</span></pre>
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