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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/gatb-core">Debian Med / gatb-core</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f">3fcc375e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-13T12:39:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.2+dfsg</pre>
</li>
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<h4>19 changed files:</h4>
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<li class="file-stats">
<a href="#fd5da61396a8376845bee5cdf71aaf3c98a888ae">
<span class="new-file">
+
.circleci/config.yml
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#4c007bda60857aed5186f73b4dd88ee753952d0d">
gatb-core/CMakeLists.txt
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<li class="file-stats">
<a href="#0b34b5f8c9585ef64fdb35942fa2a80787665e41">
gatb-core/src/gatb/bank/impl/BankComposite.hpp
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<li class="file-stats">
<a href="#13f7744556376e02feaab111f0de8ea4357e042b">
gatb-core/src/gatb/bank/impl/BankFasta.hpp
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<li class="file-stats">
<a href="#b0e9ebb304b6e44dae00765af8425ddd9a50038b">
gatb-core/src/gatb/bank/impl/BankRandom.hpp
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<li class="file-stats">
<a href="#587e8169083572229bf6c612a47fa578d0a1e078">
gatb-core/src/gatb/bank/impl/BankSplitter.hpp
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<li class="file-stats">
<a href="#0757b01aca9a4a6ea425f9fc5a1db6087ce64919">
gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp
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<li class="file-stats">
<a href="#ed783240a52e80bd1c3a470d6646b3f6b3ab63e4">
gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
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<li class="file-stats">
<a href="#0003eb464073534091790058d582096d3afebc7b">
gatb-core/src/gatb/tools/compression/HeaderCoder.cpp
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<li class="file-stats">
<a href="#6a4142b950b94fe8e7b1138f2636faed6f8c1f81">
gatb-core/src/gatb/tools/compression/Leon.hpp
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<li class="file-stats">
<a href="#22ae9527657b86b69020594ca26bd59c6e3eb5d2">
gatb-core/src/gatb/tools/math/Integer.hpp
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<li class="file-stats">
<a href="#64094465b0a91aa6c83ffc65a8bae75a47d20b5f">
gatb-core/src/gatb/tools/math/LargeInt.hpp
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<li class="file-stats">
<a href="#af60955c06c6e8087e1549eb1abc46c4349e4ffe">
gatb-core/src/gatb/tools/math/LargeInt1.pri
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<li class="file-stats">
<a href="#77b098bda12abbf057d2bf11516346f1e0a1c085">
gatb-core/src/gatb/tools/math/NativeInt64.hpp
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<li class="file-stats">
<a href="#74418ffa3a767fcad424294006ecdcf5482dbc27">
gatb-core/src/gatb/tools/math/NativeInt8.hpp
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<li class="file-stats">
<a href="#4258957fbedcdb09fe6853db03d786c2be1fbc78">
gatb-core/src/gatb/tools/misc/impl/Pool.hpp
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<li class="file-stats">
<a href="#9e55af0933f28a8ed49f8655e3be1ce7aa27b1a6">
gatb-core/thirdparty/BooPHF/BooPHF.h
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<h4>Changes:</h4>
<li id="fd5da61396a8376845bee5cdf71aaf3c98a888ae">
<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#fd5da61396a8376845bee5cdf71aaf3c98a888ae"><strong>.circleci/config.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">docker</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">debian:stretch"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">checkout</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Installing SUDO</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sudo</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">rm</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-rf</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">/var/lib/apt/lists/*'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Installing GCC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build-essential</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">wget</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">zlib1g</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">zlib1g-dev'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install CMAKE</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="s" style="color: #d14;">wget https://cmake.org/files/v3.10/cmake-3.10.2-Linux-x86_64.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="s" style="color: #d14;">tar -xvzf cmake-3.10.2-Linux-x86_64.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="s" style="color: #d14;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/ccmake</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="s" style="color: #d14;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/cmake</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="s" style="color: #d14;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/cpack</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="s" style="color: #d14;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/ctest</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="s" style="color: #d14;">DIR=$(pwd)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/ccmake /usr/bin/ccmake</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/cmake /usr/bin/cmake</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/cpack /usr/bin/cpack</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/ctest /usr/bin/ctest</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install CPPUnit</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sudo</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">libcppunit-dev'</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Creating Build Files</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">cd</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">gatb-core</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">mkdir</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cd</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cmake</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">..</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">make</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-j</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4'</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># looks like circleci charges credits so i better not run the cppunit tests..</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># - run:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># name: CPPUnit test</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># command: 'export CPPUNIT_VERBOSE=TRUE && cd gatb-core/build && ./bin/gatb-core-cppunit'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise-3.7</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span> <span class="c1" style="color: #998; font-style: italic;"># for cmake 3</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">libcppunit-dev</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-3.7</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake-data</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "`echo $CXX`" == "g++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=g++-4.8; fi</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "`echo $CXX`" == "clang++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=clang++-3.7; fi</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd gatb-core</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd build</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cmake .. && make</span> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">export CPPUNIT_VERBOSE=TRUE && ./bin/gatb-core-cppunit</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">global</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MAKEFLAGS="-j 4"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -77,7 +77,7 @@ generate the wanted artifacts:</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown">The following third parties have to be already installed to compile GATB-Core:</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"><span class="p">*</span> a <span class="gs" style="font-weight: 600;">**C++/11 capable compiler**</span> (<span class="ge" style="font-style: italic;">*e.g.*</span> gcc 4.7+, clang 3.5+, Apple/clang 6.0+)</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"><span class="p">*</span> <span class="gs" style="font-weight: 600;">**CMake 3.1+**</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">*</span> <span class="gs" style="font-weight: 600;">**CMake 3.1<span class="idiff left right">0</span>+**</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown">In addition, you could install these optional tools:</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#4c007bda60857aed5186f73b4dd88ee753952d0d"><strong>gatb-core/CMakeLists.txt</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">@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 3.10.0)</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The default version number is the latest official build</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_MAJOR 1<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_MINOR 4<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_PATCH <span class="idiff left right">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_PATCH <span class="idiff left right">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># But, it is possible to define another release number during a local build</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>DEFINED MAJOR<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#0b34b5f8c9585ef64fdb35942fa2a80787665e41"><strong>gatb-core/src/gatb/bank/impl/BankComposite.hpp</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">@@ -153,7 +153,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getCompositionNb</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_banks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \return maximum number of files. */</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">30</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">30</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Return the vector of IBank objects.</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * \return the IBank objects. */</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#13f7744556376e02feaab111f0de8ea4357e042b"><strong>gatb-core/src/gatb/bank/impl/BankFasta.hpp</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">@@ -209,7 +209,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"><span class="nl">protected:</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \return maximum number of files. */</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#b0e9ebb304b6e44dae00765af8425ddd9a50038b"><strong>gatb-core/src/gatb/bank/impl/BankRandom.hpp</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">@@ -81,7 +81,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">estimate</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">totalSize</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \return maximum number of files. */</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#587e8169083572229bf6c612a47fa578d0a1e078"><strong>gatb-core/src/gatb/bank/impl/BankSplitter.hpp</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">@@ -99,7 +99,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">estimate</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">totalSize</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \return maximum number of files. */</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#0757b01aca9a4a6ea425f9fc5a1db6087ce64919"><strong>gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp</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">@@ -119,7 +119,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo2Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"%5i:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">ii</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">_histogram</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getLength2</span><span class="p">();</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="p">{</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo2Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%6lli"</span><span class="p">,</span> <span class="n" style="color: #333;">_histogram</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get2D</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">,</span><span class="n" style="color: #333;">jj</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo2Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%6lli"</span><span class="p">,</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">_histogram</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get2D</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">,</span><span class="n" style="color: #333;">jj</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="p">}</span></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo2Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="134" 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">@@ -134,7 +134,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//output 1D histogram now</span></span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">_histogram</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getLength</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="p">{</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo1Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"%i</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lli"</span><span class="p">,</span><span class="n" style="color: #333;">ii</span><span class="p">,</span><span class="n" style="color: #333;">_histogram</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo1Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"%i</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lli"</span><span class="p">,</span><span class="n" style="color: #333;">ii</span><span class="p">,<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">_histogram</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">));</span></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="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">histo1Dfile</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> </span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#ed783240a52e80bd1c3a470d6646b3f6b3ab63e4"><strong>gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.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">@@ -81,7 +81,7 @@ namespace gatb { namespace core { namespace kmer { namespace impl {</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progressFormat0</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DSK: counting kmers "</span><span class="p">;</span></span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progressFormat1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DSK: Pass %d/%d, Step 1: partitioning "</span><span class="p">;</span></span>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progressFormat2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DSK: Pass %d/%d, Step 2: counting kmers "</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progressFormat4</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DSK: nb solid kmers<span class="idiff left right"> found </span>: %-9ld "</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progressFormat4</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DSK: nb solid kmers: %-9ld "</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*********************************************************************</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** METHOD :</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#0003eb464073534091790058d582096d3afebc7b"><strong>gatb-core/src/gatb/tools/compression/HeaderCoder.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">@@ -25,6 +25,7 @@</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#define PRINT_DEBUG_ENCODER</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#define PRINT_DEBUG_DECODER</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//====================================================================================</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -703,13 +704,10 @@ void HeaderDecoder::decodeNumeric(){</td>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">decodeNumeric</span><span class="p">(</span><span class="n" style="color: #333;">_rangeDecoder</span><span class="p">,</span> <span class="n" style="color: #333;">_numericModels</span><span class="p">[</span><span class="n" style="color: #333;">_misIndex</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_currentHeader += CompressionUtils::numberToString(value);</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">200</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span><span class="mi" style="color: #099;">200</span><span class="p">,</span><span class="s" style="color: #d14;">"%llu"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">_currentHeader</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_currentHeader += to_string(value); // C++11</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">_currentHeader</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef PRINT_DEBUG_DECODER</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Adding: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st<span class="idiff left">ring</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">temp</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Adding: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">to_string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">value</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"><span class="p">}</span></span>
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="723" 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="721" 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">@@ -723,13 +721,10 @@ void HeaderDecoder::decodeDelta(){</td>
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723
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"></span>
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724
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueFromDelta</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">_prevFieldValues</span><span class="p">[</span><span class="n" style="color: #333;">_fieldIndex</span><span class="p">],</span> <span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">200</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span><span class="mi" style="color: #099;">200</span><span class="p">,</span><span class="s" style="color: #d14;">"%llu"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="cpp"> <span class="n" style="color: #333;">_currentHeader</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_currentHeader += to_string(value);</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">_currentHeader</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="cpp"> </span>
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731
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef PRINT_DEBUG_DECODER</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Adding: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st<span class="idiff left">ring</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">temp</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Adding: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">to_string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">value</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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733
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC730" 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">@@ -742,13 +737,10 @@ void HeaderDecoder::decodeDelta2(){</td>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="cpp"> <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">decodeNumeric</span><span class="p">(</span><span class="n" style="color: #333;">_rangeDecoder</span><span class="p">,</span> <span class="n" style="color: #333;">_numericModels</span><span class="p">[</span><span class="n" style="color: #333;">_misIndex</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionUtils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueFromDelta</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">_prevFieldValues</span><span class="p">[</span><span class="n" style="color: #333;">_fieldIndex</span><span class="p">],</span> <span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">200</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span><span class="mi" style="color: #099;">200</span><span class="p">,</span><span class="s" style="color: #d14;">"%llu"</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="cpp"> <span class="n" style="color: #333;">_currentHeader</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_currentHeader += to_string(value);</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">_currentHeader</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef PRINT_DEBUG_DECODER</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Adding: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st<span class="idiff left">ring</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">temp</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Adding: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">to_string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">value</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#6a4142b950b94fe8e7b1138f2636faed6f8c1f81"><strong>gatb-core/src/gatb/tools/compression/Leon.hpp</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">@@ -462,7 +462,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">estimate</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">totalSize</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \return maximum number of files. */</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getMaxNbFiles</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"> </span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#22ae9527657b86b69020594ca26bd59c6e3eb5d2"><strong>gatb-core/src/gatb/tools/math/Integer.hpp</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">@@ -114,7 +114,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Get the size of an instance of the class used by the variant (ie. one of the Ti template class parameters)</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * \return the size of an object (in bits).</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">apply_visitor</span> <span class="p">(</span><span class="n" style="color: #333;">Integer_size</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">));</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">apply_visitor</span> <span class="p">(</span><span class="n" style="color: #333;">Integer_size</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">));</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Get the HDF5 type for the the class used by the variant (ie. one of the Ti template class parameters)</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * \param[in] isCompound : tells whether the type is composed or not</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">@@ -310,7 +310,7 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span> <span class="p">}};</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Integer_size</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">static_visitor</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">getSize</span><span class="p">();</span> <span class="p">}};</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">getSize</span><span class="p">();</span> <span class="p">}};</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Integer_plus</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">static_visitor</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">IntegerTemplate</span><span class="o" style="font-weight: 600;">></span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">IntegerTemplate</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">IntegerTemplate</span><span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p">);</span> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#64094465b0a91aa6c83ffc65a8bae75a47d20b5f"><strong>gatb-core/src/gatb/tools/math/LargeInt.hpp</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">@@ -137,7 +137,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Get the size of an instance of the class</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * \return the size of an object (in bits).</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">precision</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">precision</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Returns lower 64 bits */</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#af60955c06c6e8087e1549eb1abc46c4349e4ffe"><strong>gatb-core/src/gatb/tools/math/LargeInt1.pri</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">@@ -46,7 +46,7 @@ public:</td>
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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"> static const char* getName () { return "LargeInt<1>"; }</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"> static <span class="idiff left right">const </span>size_t getSize () { return 8*sizeof(u_int64_t); }</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> static size_t getSize () { return 8*sizeof(u_int64_t); }</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> /** Returns lower 64 bits */</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> u_int64_t toInt () const { return value; }</span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#77b098bda12abbf057d2bf11516346f1e0a1c085"><strong>gatb-core/src/gatb/tools/math/NativeInt64.hpp</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">@@ -59,7 +59,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setVal</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">NativeInt64</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NativeInt64</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">NativeInt64</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NativeInt64</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">;</span> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#74418ffa3a767fcad424294006ecdcf5482dbc27"><strong>gatb-core/src/gatb/tools/math/NativeInt8.hpp</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">@@ -51,7 +51,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">getName</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"NativeInt8"</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int8_t</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">getSize</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int8_t</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">operator</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#4258957fbedcdb09fe6853db03d786c2be1fbc78"><strong>gatb-core/src/gatb/tools/misc/impl/Pool.hpp</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">@@ -359,6 +359,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">capacity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">extraMem</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">mainbuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span><span class="p">(</span><span class="n" style="color: #333;">capacity</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">used_space</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mainbuffer</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Exception</span> <span class="p">(</span><span class="s" style="color: #d14;">"Pool reserve() failed for %lld (+ %lld extra for %d cores) bytes"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">extraMem</span><span class="p">,</span> <span class="n" style="color: #333;">_nbCores</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//should be thread safe</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f#9e55af0933f28a8ed49f8655e3be1ce7aa27b1a6"><strong>gatb-core/thirdparty/BooPHF/BooPHF.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">@@ -4,6 +4,7 @@</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma once</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cinttypes></span></span>
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7
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <climits></span></span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></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">@@ -532,11 +533,11 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma</td>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for debug purposes</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">print</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"bit array of size %ll<span class="idiff left">i: </span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"bit array of size %ll<span class="idiff left">d: </span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">_size</span><span class="p">);</span></span>
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536
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_size</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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537
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"> <span class="p">{</span></span>
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538
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" (%ll<span class="idiff left">u) "</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">ii</span><span class="p">);</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" (%ll<span class="idiff left">d) "</span></span><span class="p"><span class="idiff">,(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">ii</span><span class="p">);</span></span>
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540
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_bitArray</span><span class="p">[</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>></span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">63</span> <span class="p">)</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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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="546" 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">@@ -545,7 +546,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma</td>
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545
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"rank array : size %lu </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">_ranks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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546
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_ranks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="p">{</span></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%ll<span class="idiff left">u : %lli, "</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">_ranks</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%ll<span class="idiff left">d : %lld, "</span></span><span class="p"><span class="idiff">,(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">,(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">_ranks</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span></span>
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="p">}</span></span>
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="837" 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">@@ -836,7 +837,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma</td>
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836
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="cpp"></span>
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837
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">totalsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">totalsizeBitset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_final_hash</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">42</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">8</span> <span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// unordered map takes approx 42B per elem [personal test] (42B with uint64_t key, would be larger for other type of elem)</span></span>
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bitarray %12<span class="idiff left right">llu</span> bits (%.2f %%) (array + ranks )</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="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bitarray %12<span class="idiff left">"</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PRIu64</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span> bits (%.2f %%) (array + ranks )</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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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="cpp"> <span class="n" style="color: #333;">totalsizeBitset</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span><span class="n" style="color: #333;">totalsizeBitset</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">totalsize</span><span class="p">);</span></span>
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"final hash %12lu bits (%.2f %%) (nb in final hash %lu)</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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842
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="cpp"> <span class="n" style="color: #333;">_final_hash</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">42</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)(</span><span class="n" style="color: #333;">_final_hash</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">42</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">8</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">totalsize</span><span class="p">,</span></span>
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