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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/nanopolish">Debian Med / nanopolish</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd">64e79bf2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T06:33:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.0</pre>
</li>
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<h4>28 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b533e7cbb3f06e3619863bd2a00e4f83882b3c8e">
<span class="new-file">
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docs/source/quickstart_polya.rst
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<li class="file-stats">
<a href="#429e1529358c118c8a24ba89fb289ddd3fad88d6">
<span class="new-file">
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etc/r9-models/r9.4_450bps.gpc.6mer.template.model
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<li class="file-stats">
<a href="#a354eabac401b7f4ebb3a6bff8bfceafc31d80d9">
scripts/nanopolish_makerange.py
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<li class="file-stats">
<a href="#64a18d231424dfe0512d5d98702a6936dd2080e2">
src/alignment/nanopolish_eventalign.cpp
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<li class="file-stats">
<a href="#10a288b7d12780ba9b509b77643a7f1d133f8a2a">
<span class="new-file">
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src/builtin_models/r9_4_450bps_gpc_6mer_template_model.inl
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<li class="file-stats">
<a href="#63a5131b4e7d1b5ad9842ac4e7b43e6cefaba190">
src/common/nanopolish_alphabet.cpp
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<a href="#2c2d378f3c858273fcc789072d022d51957e8a98">
src/common/nanopolish_alphabet.h
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<li class="file-stats">
<a href="#58a43c64ead5187f569b28ec5ca98b313c48d7c7">
src/common/nanopolish_common.h
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<li class="file-stats">
<a href="#af0c7b92cdf7a0cc7d98c3103b7fba80623a54e1">
src/common/nanopolish_fast5_io.cpp
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<li class="file-stats">
<a href="#a6b650afca4ceb444770725cd6e17939daeec862">
src/common/nanopolish_fast5_io.h
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<li class="file-stats">
<a href="#149ac5b0310ff017664f0645808befe6bda2ed83">
src/common/nanopolish_variant.cpp
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<li class="file-stats">
<a href="#125985123a25635dc9e1a81a7b2849a0f12aa286">
src/nanopolish_call_methylation.cpp
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<li class="file-stats">
<a href="#2d62e059707d17d6d88d86a4af4fce9c4c482e3d">
src/nanopolish_index.cpp
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<li class="file-stats">
<a href="#9e1d6734082431b228580bb425603ab97d4c9d1d">
src/nanopolish_methyltrain.cpp
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<li class="file-stats">
<a href="#a9c87dc87f669219ca843a7b27aba683ef12b563">
src/nanopolish_raw_loader.cpp
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<li class="file-stats">
<a href="#7c87ffe15195ab460f3be130ef4d8324408853f0">
src/nanopolish_read_db.cpp
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<li class="file-stats">
<a href="#244f2077b9e28a5e6394deda0b7574b0f80f501c">
src/nanopolish_squiggle_read.cpp
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<li class="file-stats">
<a href="#0cd5a7898ca2515cf6be03b2013fef5dda71d2cd">
src/nanopolish_squiggle_read.h
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<li class="file-stats">
<a href="#8a4594db09bdbd5859ea2b82ef08bae7e6cb4eba">
src/nanopolish_vcf2fasta.cpp
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<li class="file-stats">
<a href="#9186045b065422025ead086f2c07e4e27cd22c5e">
src/pore_model/nanopolish_builtin_models.h
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<li class="file-stats">
<a href="#40876473fea5fd59223a4e217ab3ce88ac23e944">
src/thirdparty/scrappie/scrappie_common.c
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<a href="#eb73e696473ddc8d63df1f5a3399724c99cfa0da">
<span class="deleted-file">
−
src/thirdparty/scrappie/sse_mathfun.h
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<a href="#1b1d273af27cf998f7a24ba41cfa22a7da674993">
<span class="deleted-file">
−
src/thirdparty/scrappie/util.c
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<li class="file-stats">
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<span class="deleted-file">
−
src/thirdparty/scrappie/util.h
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<li class="file-stats">
<a href="#4547105bf53f4c152441673b657f1f5a56f0b6fd">
src/training_core.cpp
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># travis.yml for github.com/jts/nanopolish</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></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: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="no" style="color: teal;">false</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">generic</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: teal;">cache</span><span class="pi">:</span> <span class="s" style="color: #d14;">apt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><span class="na" style="color: teal;">git</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: teal;">depth</span><span class="pi">:</span> <span class="s" style="color: #d14;">1</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"><span class="na" style="color: teal;">matrix</span><span class="pi">:</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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: teal;">include</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">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Set env for both nanoplish and the dependency hdf5.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">env</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;">CC=gcc-4.8</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;">CXX=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;">AR=gcc-ar-4.8</span></span>
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17
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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;">NM=gcc-nm-4.8</span></span>
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18
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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;">RANLIB=gcc-ranlib-4.8</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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20
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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;">CC=gcc-8</span></span>
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21
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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;">CXX=g++-8</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">AR=gcc-ar-8</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">NM=gcc-nm-8</span></span>
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24
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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;">RANLIB=gcc-ranlib-8</span></span>
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4
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"></span>
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5
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Install and export newer gcc</span></span>
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6
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"><span class="na" style="color: teal;">before_install</span><span class="pi">:</span></span>
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7
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28
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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;">sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test</span></span>
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8
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get update -qq</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install -qq g++-4.8</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="no" style="color: teal;">if [[ "${CC}" =~ ^gcc- ]]; then</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="no" style="color: teal;">echo "Installing ${CC}."</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="no" style="color: teal;">sudo apt-get install -qq "${CC}"</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="no" style="color: teal;">fi</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="no" style="color: teal;">if [[ "${CXX}" =~ ^g\+\+- ]]; then</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="no" style="color: teal;">echo "Installing ${CXX}."</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="no" style="color: teal;">sudo apt-get install -qq "${CXX}"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="no" style="color: teal;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">make CXX=g++-4.8 nanopolish && make CXX=g++-4.8 test</span></span></pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Suppress all compiler warnings for hdf5 Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># to display the log without downloading the raw log on Travis log page.</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Travis finishs with error when exceeding the limit of 4 MB of log length.</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export H5_CFLAGS="-w"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make && make test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -8,17 +8,21 @@ SUBDIRS := src src/hmm src/thirdparty src/thirdparty/scrappie src/common src/ali</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#Basic flags every build needs</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="nv" style="color: teal;">LIBS</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="nt" style="color: navy;">-lz</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nv" style="color: teal;">LIBS</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nt" style="color: navy;">-lz</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-O3</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: navy;">-fopenmp</span> <span class="nt" style="color: navy;">-fsigned-char</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c99</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: navy;">-fopenmp</span> <span class="nt" style="color: navy;">-fsigned-char</span><span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">-D_FILE_OFFSET_BITS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">64 </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right">#D_FILE_OFFSET_BITS=64 makes nanopolish work in 32 bit systems</span></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c99<span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">-fsigned-char</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-D_FILE_OFFSET_BITS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">64 </span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="nv" style="color: teal;">CXX</span> <span class="o" style="font-weight: 600;">?=</span> g++</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nv" style="color: teal;">CC</span> <span class="o" style="font-weight: 600;">?=</span> gcc</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Change the value of HDF5, EIGEN, or HTS below to any value to disable compilation of bundled code</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="make"><span class="nv" style="color: teal;">HDF5</span><span class="o" style="font-weight: 600;">?=</span><span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"><span class="nv" style="color: teal;">EIGEN</span><span class="o" style="font-weight: 600;">?=</span><span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">HTS</span><span class="o" style="font-weight: 600;">?=</span><span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="nv" style="color: teal;">HDF5</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nv" style="color: teal;">EIGEN</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">HTS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="nv" style="color: teal;">HDF5_VERSION</span> <span class="o" style="font-weight: 600;">?=</span> 1.8.14</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="nv" style="color: teal;">HDF5_CONFIG_ARGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: navy;">--enable-threadsafe</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"><span class="nv" style="color: teal;">EIGEN_VERSION</span> <span class="o" style="font-weight: 600;">?=</span> 3.2.5</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Check operating system, OSX doesn't have -lrt</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"><span class="nv" style="color: teal;">UNAME_S</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">uname</span> <span class="nt" style="color: navy;">-s</span><span class="nv" style="color: teal;">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,52 +32,53 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Default to automatically installing hdf5</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(HDF5),</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">install)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"> <span class="nv" style="color: teal;">H5_LIB</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>./lib/libhdf5.a</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"> <span class="nv" style="color: teal;">H5_INCLUDE</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="nt" style="color: navy;">-I</span>./include</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="make"> <span class="nv" style="color: teal;">H5_LIB</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>./lib/libhdf5.a</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="nv" style="color: teal;">H5_INCLUDE</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nt" style="color: navy;">-I</span>./include</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"> <span class="nv" style="color: teal;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-ldl</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Use system-wide hdf5</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"> <span class="nv" style="color: teal;">H5_LIB</span><span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"> <span class="nv" style="color: teal;">H5_INCLUDE</span><span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> <span class="nv" style="color: teal;">H5_LIB</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"> <span class="nv" style="color: teal;">H5_INCLUDE</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span></span>
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38
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"> <span class="nv" style="color: teal;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-lhdf5</span></span>
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39
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></span>
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41
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Default to automatically installing EIGEN</span></span>
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42
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(EIGEN),</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">install)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="make"> <span class="nv" style="color: teal;">EIGEN_CHECK</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>eigen/INSTALL</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"> <span class="nv" style="color: teal;">EIGEN_CHECK</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>eigen/INSTALL</span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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45
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Use system-wide eigen</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="make"> <span class="nv" style="color: teal;">EIGEN_CHECK</span><span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="make"> <span class="nv" style="color: teal;">EIGEN_CHECK</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Default to build and link the libhts submodule</span></span>
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50
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(HTS),</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">install)</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_LIB</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>./htslib/libhts.a</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_INCLUDE</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="nt" style="color: navy;">-I</span>./htslib</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_LIB</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>./htslib/libhts.a</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_INCLUDE</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nt" style="color: navy;">-I</span>./htslib</span>
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53
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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54
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Use system-wide htslib</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_LIB</span><span class="o" style="font-weight: 600;">=</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_INCLUDE</span><span class="o" style="font-weight: 600;">=</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_LIB</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="make"> <span class="nv" style="color: teal;">HTS_INCLUDE</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span></span>
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57
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"> <span class="nv" style="color: teal;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-lhts</span></span>
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58
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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59
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"></span>
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60
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Include the header-only fast5 library</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="make"><span class="nv" style="color: teal;">FAST5_INCLUDE</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="nt" style="color: navy;">-I</span>./fast5/include</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="make"><span class="nv" style="color: teal;">FAST5_INCLUDE</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nt" style="color: navy;">-I</span>./fast5/include</span>
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62
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"></span>
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63
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Include the header-only eigen library</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="make"><span class="nv" style="color: teal;">EIGEN_INCLUDE</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="nt" style="color: navy;">-I</span>./eigen/</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="make"><span class="nv" style="color: teal;">EIGEN_INCLUDE</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nt" style="color: navy;">-I</span>./eigen/</span>
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65
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"></span>
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66
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Include the src subdirectories</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="make"><span class="nv" style="color: teal;">NP_INCLUDE</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix <span class="nt" style="color: navy;">-I</span>./, <span class="nv" style="color: teal;">$(SUBDIRS)</span><span class="o" style="font-weight: 600;">)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="make"><span class="nv" style="color: teal;">NP_INCLUDE</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix <span class="nt" style="color: navy;">-I</span>./, <span class="nv" style="color: teal;">$(SUBDIRS)</span><span class="o" style="font-weight: 600;">)</span></span>
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68
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="make"></span>
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69
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Add include flags</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$(H5_INCLUDE)</span> <span class="nv" style="color: teal;">$(HTS_INCLUDE)</span> <span class="nv" style="color: teal;">$(FAST5_INCLUDE)</span> <span class="nv" style="color: teal;">$(NP_INCLUDE)</span> <span class="nv" style="color: teal;">$(EIGEN_INCLUDE)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Main programs to build</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="make"><span class="nv" style="color: teal;">PROGRAM</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>nanopolish</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="make"><span class="nv" style="color: teal;">TEST_PROGRAM</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>nanopolish_test</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="make"><span class="nv" style="color: teal;">PROGRAM</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>nanopolish</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="make"><span class="nv" style="color: teal;">TEST_PROGRAM</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>nanopolish_test</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PROGRAM) $(TEST_PROGRAM)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">depend $(PROGRAM)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Build libhts</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">@@ -85,16 +90,23 @@ htslib/libhts.a:</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># If this library is a dependency the user wants HDF5 to be downloaded and built.</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="make"><span class="nl">lib/libhdf5.a</span><span class="o" style="font-weight: 600;">:</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> hdf5-1.8.14.tar.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span>wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="make"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xzf</span> hdf5-1.8.14.tar.gz <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>255</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>hdf5-1.8.14 <span class="o" style="font-weight: 600;">&&</span> ./configure <span class="nt" style="color: navy;">--enable-threadsafe</span> <span class="nt" style="color: navy;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/.. <span class="o" style="font-weight: 600;">&&</span> make <span class="o" style="font-weight: 600;">&&</span> make <span class="nb" style="color: #0086b3;">install</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> hdf5-<span class="nv" style="color: teal;">$(HDF5_VERSION)</span>.tar.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="make"> <span class="nv" style="color: teal;">version_major_minior</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$(HDF5_VERSION)</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-E</span> <span class="s1" style="color: #d14;">'s/\.[0-9]+$$//'</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="make"> wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-<span class="nv" style="color: teal;">$$</span><span class="o" style="font-weight: 600;">{</span>version_major_minior<span class="o" style="font-weight: 600;">}</span>/hdf5-<span class="nv" style="color: teal;">$(HDF5_VERSION)</span>/src/hdf5-<span class="nv" style="color: teal;">$(HDF5_VERSION)</span>.tar.gz<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>
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91
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<td class="diff-line-num new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="make"></span>
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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tar</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-xzf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">hdf5-$(HDF5_VERSION).tar.gz</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">exit</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">255</span></span>
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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">cd</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">hdf5-$(HDF5_VERSION)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">./configure</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">--enable-threadsafe</span> <span class="nv" style="color: teal;">--libdir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/../lib <span class="nt" style="color: navy;">--includedir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/../include <span class="nt" style="color: navy;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/.. <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="make"> make <span class="o" style="font-weight: 600;">&&</span> make <span class="nb" style="color: #0086b3;">install</span></span>
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92
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="93" 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">
93
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Download and install eigen if not already downloaded</span></span>
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<td class="diff-line-num old_line" data-linenumber="94" 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">
94
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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="make"><span class="nl">eigen/INSTALL</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> 3.2.5.tar.bz2 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span>wget http://bitbucket.org/eigen/eigen/get/3.2.5.tar.bz2<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="make"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xjvf</span> 3.2.5.tar.bz2 <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>255</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv </span>eigen-eigen-bdd17ee3b1b3 eigen <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>255</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> <span class="nv" style="color: teal;">$(EIGEN_VERSION)</span>.tar.bz2 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="make"> wget http://bitbucket.org/eigen/eigen/get/<span class="nv" style="color: teal;">$(EIGEN_VERSION)</span>.tar.bz2<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="make"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xjf</span> <span class="nv" style="color: teal;">$(EIGEN_VERSION)</span>.tar.bz2 <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>255</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv </span>eigen-eigen-<span class="k" style="font-weight: 600;">*</span> eigen <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>255</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
98
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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="make"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Source files</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,22 +115,20 @@ eigen/INSTALL:</td>
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103
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Find the source files by searching subdirectories</span></span>
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104
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="make"><span class="nv" style="color: teal;">CPP_SRC</span> <span class="o" style="font-weight: 600;">:=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>foreach <span class="nb" style="color: #0086b3;">dir</span>, <span class="nv" style="color: teal;">$(SUBDIRS)</span>, <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard <span class="nv" style="color: teal;">$(dir)</span>/<span class="k" style="font-weight: 600;">*</span>.cpp<span class="o" style="font-weight: 600;">))</span></span>
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105
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="make"><span class="nv" style="color: teal;">C_SRC</span> <span class="o" style="font-weight: 600;">:=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>foreach <span class="nb" style="color: #0086b3;">dir</span>, <span class="nv" style="color: teal;">$(SUBDIRS)</span>, <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard <span class="nv" style="color: teal;">$(dir)</span>/<span class="k" style="font-weight: 600;">*</span>.c<span class="o" style="font-weight: 600;">))</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="make"><span class="nv" style="color: teal;">EXE_SRC</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span>src/main/nanopolish.cpp src/test/nanopolish_test.cpp</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="make"><span class="nv" style="color: teal;">EXE_SRC</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>src/main/nanopolish.cpp src/test/nanopolish_test.cpp</span>
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107
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="make"></span>
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108
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Automatically generated object names</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="make"><span class="nv" style="color: teal;">CPP_OBJ</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>CPP_SRC:.cpp<span class="o" style="font-weight: 600;">=</span>.o<span class="o" style="font-weight: 600;">)</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="make"><span class="nv" style="color: teal;">C_OBJ</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>C_SRC:.c<span class="o" style="font-weight: 600;">=</span>.o<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="make"><span class="nv" style="color: teal;">CPP_OBJ</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>CPP_SRC:.cpp<span class="o" style="font-weight: 600;">=</span>.o<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="make"><span class="nv" style="color: teal;">C_OBJ</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>C_SRC:.c<span class="o" style="font-weight: 600;">=</span>.o<span class="o" style="font-weight: 600;">)</span></span>
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111
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="make"></span>
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112
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Generate dependencies</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="make"><span class="nv" style="color: teal;"><span class="idiff left">PHONY</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span>depend</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="make"><span class="nl"><span class="idiff left">.PHONY</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="nf" style="color: #900; font-weight: 600;">depend</span></span>
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114
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="make"><span class="nl">depend</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">.depend</span></span>
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115
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="make"></span>
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116
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="make"><span class="nl">.depend</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(CPP_SRC) $(C_SRC) $(EXE_SRC) $(H5_LIB) $(EIGEN_CHECK)</span></span>
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117
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> ./.depend</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="make"> <span class="nv" style="color: teal;">$(CXX)</span> <span class="nv" style="color: teal;">$(CXXFLAGS)</span> <span class="nv" style="color: teal;">$(CPPFLAGS)</span> <span class="nt" style="color: navy;">-MM</span> <span class="nv" style="color: teal;">$(CPP_SRC)</span> <span class="nv" style="color: teal;">$(C_SRC)</span> <span class="o" style="font-weight: 600;">></span> ./.depend<span class="p">;</span></span>
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119
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">include</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">.depend</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Compile objects</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="make"><span class="nl">.cpp.o</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="make"> <span class="nv" style="color: teal;">$(CXX)</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span> <span class="nt" style="color: navy;">-c</span> <span class="nv" style="color: teal;">$(CXXFLAGS)</span> <span class="nv" style="color: teal;">$(CPPFLAGS)</span> <span class="nt" style="color: navy;">-fPIC</span> <span class="nv" style="color: teal;">$<</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="144" 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">@@ -134,8 +144,11 @@ $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(EIG</td>
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134
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"><span class="nl">$(TEST_PROGRAM)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/test/nanopolish_test.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB)</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"> <span class="nv" style="color: teal;">$(CXX)</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span> <span class="nv" style="color: teal;">$(CXXFLAGS)</span> <span class="nv" style="color: teal;">$(CPPFLAGS)</span> <span class="nt" style="color: navy;">-fPIC</span> <span class="nv" style="color: teal;">$<</span> <span class="nv" style="color: teal;">$(CPP_OBJ)</span> <span class="nv" style="color: teal;">$(C_OBJ)</span> <span class="nv" style="color: teal;">$(HTS_LIB)</span> <span class="nv" style="color: teal;">$(H5_LIB)</span> <span class="nv" style="color: teal;">$(LIBS)</span> <span class="nv" style="color: teal;">$(LDFLAGS)</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test</span></span>
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137
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(TEST_PROGRAM)</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="make"> ./<span class="nv" style="color: teal;">$(TEST_PROGRAM)</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$(PROGRAM)</span> <span class="nv" style="color: teal;">$(TEST_PROGRAM)</span> <span class="nv" style="color: teal;">$(CPP_OBJ)</span> <span class="nv" style="color: teal;">$(C_OBJ)</span> src/main/nanopolish.o src/test/nanopolish_test.o</span></pre>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$(PROGRAM)</span> <span class="nv" style="color: teal;">$(TEST_PROGRAM)</span> <span class="nv" style="color: teal;">$(CPP_OBJ)</span> <span class="nv" style="color: teal;">$(C_OBJ)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="make"> src/main/nanopolish.o src/test/nanopolish_test.o</span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#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">@@ -6,6 +6,8 @@ Software package for signal-level analysis of Oxford Nanopore sequencing data. N</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Release notes</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> 0.11.0: support for multi-fast5 files. <span class="sb" style="color: #d14;">`nanopolish methyltrain`</span> now subsamples input data, improving speed and memory usage</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">*</span> 0.10.2: added new program <span class="sb" style="color: #d14;">`nanopolish polya`</span> to estimate the length of poly-A tails on direct RNA reads (by @paultsw)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">*</span> 0.10.1: <span class="sb" style="color: #d14;">`nanopolish variants --consensus`</span> now only outputs a VCF file instead of a fasta sequence. The VCF file describes the changes that need to be made to turn the draft sequence into the polished assembly. A new program, <span class="sb" style="color: #d14;">`nanopolish vcf2fasta`</span>, is provided to generate the polished genome (this replaces <span class="sb" style="color: #d14;">`nanopolish_merge.py`</span>, see usage instructions below). This change is to avoid issues when merging segments that end on repeat boundaries (reported by Michael Wykes and Chris Wright).</span>
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<li id="b533e7cbb3f06e3619863bd2a00e4f83882b3c8e">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#b533e7cbb3f06e3619863bd2a00e4f83882b3c8e"><strong>docs/source/quickstart_polya.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _quickstart_polya:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Quickstart - how to estimate poly(A) tail lengths from nanopore native RNA reads</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">=================================================================================</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Owing to homopolymer effects and the proximity to the sequencing adapters, the polyadenylated tails of reads obtained from nanopore native RNA sequencing are improperly basecalled, making their lengths difficult to quantify. We developed the `polya` subprogram to use an alternative statistical model to estimate these tail lengths.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">In this quickstart tutorial, we'll show you how to estimate polyadenylated tail lengths step-by-step, starting from nothing but raw fast5 files. We'll basecall the fast5 files with Oxford Nanopore Technologies' *albacore* basecaller, before aligning the resulting reads with *minimap2*, indexing the files with *nanopolish index*, and finally segmenting the reads and calling the tail lengths with *nanopolish polya*.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">We'll be following the steps taken in our `benchmarking analysis <https://github.com/paultsw/polya_analysis>`_ workflow that accompanies `our publication <https://www.biorxiv.org/content/early/2018/11/09/459529>`_. In each step below, we'll generate files in the working directory instead of making subdirectories, except in the case of large datasets.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Software requirements</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">---------------------</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">* `nanopolish <https://github.com/jts/nanopolish>`_ `>= v10.2`</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">* `minimap2 <https://github.com/lh3/minimap2>`_ `>= v2.12`</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">* `samtools <http://www.htslib.org/>`_ `>= v1.9`</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* `albacore >= v2.3.3` (from Oxford Nanopore's private customer portal)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Download raw fast5 data and basecall</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Let's start by downloading a dataset of fast5 files from the European Nucleotide Archive. We'll download a tarball of fast5 files containing reads that are known to have polyadenylated tail lengths of 30nt. ::</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> mkdir data && mkdir data/fastqs</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> wget ftp://ftp.sra.ebi.ac.uk/vol1/ERA158/ERA1580896/oxfordnanopore_native/30xpolyA.tar.gz -O 30xpolyA.tar.gz && mv 30xpolyA.tar.gz data/</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> tar -xzf data/30xpolyA.tar.gz -C data/</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> read_fast5_basecaller.py --worker_threads=8 -f FLO-MIN107 -k SQK-RNA001 -q 0 -s data/fastqs -i data/30xpolyA/fast5/pass</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> cat data/fastqs/workspace/pass/*.fastq > data/30xpolyA.fastq</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">In the above, change the value of the `-f` and `-k` arguments based on your flow-cell and sequencing kit, as the basecaller's accuracy is highly dependent upon these settings.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Our directory structure should now look something like this: ::</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> (current directory)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> |- data/</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> |-- 30xpolyA.fastq</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> |-- 30xpolyA.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> |-- 30xpolyA/</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> |--- fast5/</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> |---- pass/</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> |----- raw_read1.fast5</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> |----- (... more raw fast5's here ...)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> |-- fastqs/</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> |--- workspace/</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> |---- pass/</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Index with nanopolish index</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">---------------------------</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Let's construct an index for our reads with nanopolish's `index` subprogram. This constructs a fast lookup table that tells our program where to find the raw fast5 file for each</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">basecalled read. ::</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"> nanopolish index --directory=data/30xpolyA/fast5/pass --sequencing-summary=data/fastqs/sequencing_summary.txt data/30xpolyA.fastq</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">This should generate a collection of files in the same directory that contains the `30xpolyA.fastq`.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Align with minimap2 and format the BAM file</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">-------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Now we'll align our basecalled mRNA sequences in the fastq file with our reference. First download a reference fasta: ::</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> wget https://raw.githubusercontent.com/paultsw/polya_analysis/master/data/references/enolase_reference.fas</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> wget https://raw.githubusercontent.com/paultsw/polya_analysis/master/data/references/enolase_reference.fai</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> mv enolase_reference.* data/</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Note that our directory structure should now look like this: ::</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> (current directory)</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> |- data/</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> |-- enolase_reference.fas</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> |-- enolase_reference.fai</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> |-- (... same structure as above ...)</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Let's run `minimap2` to align our basecalled reads to this reference and generate a collection of SAM/BAM files with `samtools`: ::</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> minimap2 -a -x map-ont data/enolase_reference.fas data/30xpolyA.fastq | samtools view -b - -o data/30xpolyA.bam</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> cd data && samtools sort -T tmp -o 30xpolyA.sorted.bam 30xpolyA.bam && samtools index 30xpolyA.sorted.bam && cd ..</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">Note that we used `-x map-ont`, which is typically for unspliced reads (e.g. genomic DNA) coming from nanopore sequencers. In typical native mRNA sequencing, you should use `-x splice`,</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">which is a splice-aware setting (and uses a different gap cost in the alignment). We're using `map-ont` due to the fact that our reads come from a control dataset with no splicing.</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">There should be three more files in the `data` directory now: `30xpolyA.bam`, `30xpolyA.sorted.bam`, and `30xpolyA.sorted.bam.bai`.</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">Segmentation and tail length estimation with nanopolish polya</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">-------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Finally, we can run the polyadenylation estimator: ::</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> nanopolish polya --threads=8 --reads=data/30xpolyA.fastq --bam=data/30xpolyA.sorted.bam --genome=data/enolase_reference.fas > polya_results.tsv</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">Set the `--threads` flag to the number of parallel threads you want to use. Generally speaking, a larger number of threads tends to lower the compute time, but there are diminishing</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">returns to a higher value and performance can actually decrease if your CPU is incapable of supporting your desired number of parallel threads. The best number of threads to use is</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">highly dependent upon your hardware.</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">Interpreting the output TSV file</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">--------------------------------</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">We'll end this quickstart with a look at the output of the polya program. Let's look at the top five lines of the `polya_results.tsv` file we've just generated: ::</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> head -20 polya_results.tsv | column -t</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> readname contig position leader_start adapter_start polya_start transcript_start read_rate polya_length qc_tag</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> d6f42b79-90c6-4edd-8c8f-8a7ce0ac6ecb YHR174W 0 54.0 3446.0 7216.0 8211.0 130.96 38.22 PASS</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> 453f3f3e-d22f-4d9c-81a6-8576e23390ed YHR174W 0 228.0 5542.0 10298.0 11046.0 130.96 27.48 PASS</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> e02d9858-0c04-4d86-8dba-18a47d9ac005 YHR174W 0 221.0 1812.0 7715.0 8775.0 97.16 29.16 PASS</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> b588dee2-2c5b-410c-91e1-fe8140f4f837 YHR174W 0 22.0 8338.0 13432.0 14294.0 130.96 32.43 PASS</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> af9dfee2-1711-4083-b109-487b99895e0a YHR174W 0 889.0 3679.0 6140.0 7168.0 130.96 39.65 PASS</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> 93f98a86-3b18-48cf-8c4d-15cf277911e2 YHR174W 0 144.0 1464.0 5615.0 6515.0 120.48 30.96 SUFFCLIP</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> af9dfee2-1711-4083-b109-487b99895e0a YHR174W 0 889.0 3679.0 6140.0 7168.0 130.96 39.65 SUFFCLIP</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> 93f98a86-3b18-48cf-8c4d-15cf277911e2 YHR174W 0 144.0 1464.0 5615.0 6515.0 120.48 30.96 PASS</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> ca8d4059-9d82-45ee-aa07-4b8b351618b3 YHR174W 0 1.0 2157.0 4255.0 5862.0 111.56 54.48 PASS</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> 3493c123-78d4-4f7c-add0-cbb249aef00a YHR174W 0 78.0 1938.0 4829.0 5491.0 136.91 25.05 PASS</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> f5ff1802-3fdd-479a-8888-c72de01bbaea YHR174W 0 150.0 3476.0 7233.0 7932.0 130.96 25.35 PASS</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> bb929728-2ed8-42b0-a5a5-eea4bfd62673 YHR174W 0 91.0 1061.0 6241.0 6910.0 111.56 19.74 PASS</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> 17cf3fef-1acb-4045-8252-e9c00fedfb7c YHR174W 0 447.0 6004.0 20058.0 20964.0 100.40 25.17 ADAPTER</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> 56c116d7-9286-4b57-8329-e74928b11b38 YHR174W 0 13.0 1516.0 5845.0 6773.0 130.96 35.30 PASS</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> 5ca1392c-c48f-4135-85d3-271bd4ee7a13 YHR174W 0 1.0 1976.0 4854.0 5947.0 136.91 44.64 PASS</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> 66b5a0ef-b8e6-475e-bf20-04b96154a67f YHR174W 0 98.0 3847.0 7066.0 7925.0 120.48 29.32 PASS</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> 34bf2187-5816-4744-8e6a-3250b5247e02 YHR174W 0 1.0 2897.0 6885.0 7547.0 125.50 22.54 PASS</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">Each row corresponds to the output for a given read. The columns have the following interpretation:</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">* `readname` refers to the unique ID associated to this particular read. This string is also used to look up the corresponding fast5 file, e.g. by looking</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> through the `readdb` file generated by `nanopolish index`.</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">* `contig` refers to the reference sequence that this read aligns to, and is taken from the BAM file.</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">* `position` is the 5' starting position of the alignment to the reference sequence, and also comes from the BAM file.</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">* `leader_start`, `adapter_start`, `polya_start`, and `transcript_start` are the indices of the signal segmentation generated by the underlying model within</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> `nanopolish`. Briefly, there are four biologically-meaningful regions of the raw sequence of electrical current readings within each fast5 file; these four</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> entries denote the starting index of each of these consecutive regions. The indices start from 0 and are oriented in the 3'-to-5' direction (due to the</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> inherent orientation of the native RNA nanopore sequencing protocol). A full exposition of this segmentation algorithm is available in the</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> `supplementary note<https://www.biorxiv.org/content/biorxiv/suppl/2018/11/09/459529.DC1/459529-2.pdf>`_ to our associated publication.</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">* `read_rate` is the estimated translocation rate (in units of nucleotides/second) of the read through the pore. The translocation rate is non-uniform during</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> the sequencing process of even a single molecule, so this is ultimately a summary statistic of the dynamic, time-varying rate.</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">* `polya_length` is the estimated polyadenylated tail length, in number of nucleotides. That this value is a float rather than an integer reflects the fact</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> that our estimated tail length is the output of an estimator based on the translocation rate.</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">* `qc_tag` is an additional flag used to indicate the validity of the estimate. Generally speaking, you should only use rows of the output file with this value</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> set to `PASS`; all other rows with (e.g.) the `qc_tag` set to `SUFFCLIP`, `ADAPTER`, etc. display signs of irregularity that indicate that we believe the</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> estimate to be unreliable. You can easily filter away all rows with the tag set to anything other than `PASS` using a `grep`: ::</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> grep 'PASS' polya_results.tsv > polya_results.pass_only.tsv</span></pre>
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<li id="429e1529358c118c8a24ba89fb289ddd3fad88d6">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#429e1529358c118c8a24ba89fb289ddd3fad88d6"><strong>etc/r9-models/r9.4_450bps.gpc.6mer.template.model</strong></a>
The diff for this file was not included because it is too large.
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<li id="a354eabac401b7f4ebb3a6bff8bfceafc31d80d9">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#a354eabac401b7f4ebb3a6bff8bfceafc31d80d9"><strong>scripts/nanopolish_makerange.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#64a18d231424dfe0512d5d98702a6936dd2080e2"><strong>src/alignment/nanopolish_eventalign.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">@@ -243,7 +243,11 @@ void emit_tsv_header(FILE* fp)</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">emit_sam_header</span><span class="p">(</span><span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_hdr_write</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_write</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><</span> <span class="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="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error writing sam header</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="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cigar_ops_to_string</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">ops</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="386" 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">@@ -382,7 +386,12 @@ void emit_event_alignment_sam(htsFile* fp,</td>
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382
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">stride</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">().</span><span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_aux_append</span><span class="p">(</span><span class="n" style="color: #333;">event_record</span><span class="p">,</span> <span class="s" style="color: #d14;">"ES"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stride</span><span class="p">));</span></span>
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384
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_write1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">base_hdr</span><span class="p">,</span> <span class="n" style="color: #333;">event_record</span><span class="p">);</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_write1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">base_hdr</span><span class="p">,</span> <span class="n" style="color: #333;">event_record</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><</span> <span class="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="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error writing sam record</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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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">event_record</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// automatically frees malloc'd segment</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"><span class="p">}</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"></span>
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<li id="10a288b7d12780ba9b509b77643a7f1d133f8a2a">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#10a288b7d12780ba9b509b77643a7f1d133f8a2a"><strong>src/builtin_models/r9_4_450bps_gpc_6mer_template_model.inl</strong></a>
The diff for this file was not included because it is too large.
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#63a5131b4e7d1b5ad9842ac4e7b43e6cefaba190"><strong>src/common/nanopolish_alphabet.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,6 +94,39 @@ const char* MethylCpGAlphabet::_recognition_sites[] = { "CG" };</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylCpGAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_recognition_sites_methylated</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">"MG"</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylCpGAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_recognition_sites_methylated_complement</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">"GM"</span> <span class="p">};</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// methyl-cytosine in GC context</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_rank</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="p">};</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"gpc"</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;">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;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGMT"</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_complement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TGCGA"</span><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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">MethylGpCAlphabet</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="mi" style="color: #099;">5</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_num_recognition_sites</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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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_recognition_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_recognition_sites</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">"GC"</span> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_recognition_sites_methylated</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">"GM"</span> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_recognition_sites_methylated_complement</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">"MG"</span> <span class="p">};</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"></span>
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97
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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98
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Dam methylation: methyl-adenine in GATC context</span></span>
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99
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="163" 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="196" 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">@@ -163,6 +196,7 @@ const char* MethylDcmAlphabet::_recognition_sites_methylated_complement[] = { "G</td>
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163
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Global objects</span></span>
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164
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"><span class="n" style="color: #333;">DNAAlphabet</span> <span class="n" style="color: #333;">gDNAAlphabet</span><span class="p">;</span></span>
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165
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"><span class="n" style="color: #333;">MethylCpGAlphabet</span> <span class="n" style="color: #333;">gMCpGAlphabet</span><span class="p">;</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"><span class="n" style="color: #333;">MethylGpCAlphabet</span> <span class="n" style="color: #333;">gMethylGpCAlphabet</span><span class="p">;</span></span>
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166
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"><span class="n" style="color: #333;">MethylDamAlphabet</span> <span class="n" style="color: #333;">gMethylDamAlphabet</span><span class="p">;</span></span>
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167
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"><span class="n" style="color: #333;">MethylDcmAlphabet</span> <span class="n" style="color: #333;">gMethylDcmAlphabet</span><span class="p">;</span></span>
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168
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"><span class="n" style="color: #333;">UtoTRNAAlphabet</span> <span class="n" style="color: #333;">gUtoTRNAAlphabet</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,6 +205,7 @@ std::vector<const Alphabet*> get_alphabet_list()</td>
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171
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"><span class="p">{</span></span>
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172
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gDNAAlphabet</span><span class="p">,</span> </span>
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173
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gMCpGAlphabet</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gMethylGpCAlphabet</span><span class="p">,</span></span>
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174
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gMethylDamAlphabet</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gMethylDcmAlphabet</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gUtoTRNAAlphabet</span> <span class="p">};</span></span>
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<li id="2c2d378f3c858273fcc789072d022d51957e8a98">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#2c2d378f3c858273fcc789072d022d51957e8a98"><strong>src/common/nanopolish_alphabet.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">@@ -355,6 +355,26 @@ struct MethylCpGAlphabet : public Alphabet</td>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="c"> <span class="p">}</span></span>
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c"><span class="p">};</span></span>
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// methyl-cytosine in GC context</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">Alphabet</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// member variables, expanded by macrocs</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">BASIC_MEMBER_BOILERPLATE</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="c"> <span class="n" style="color: #333;">METHYLATION_MEMBER_BOILERPLATE</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// member functions</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="c"> <span class="n" style="color: #333;">BASIC_ACCESSOR_BOILERPLATE</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="c"> <span class="n" style="color: #333;">METHYLATION_ACCESSOR_BOILERPLATE</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// does this alphabet contain all of the nucleotides in bases?</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">contains_all</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bases</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="LC373" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strspn</span><span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">,</span> <span class="n" style="color: #333;">_base</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Dam methylation: methyl-adenine in GATC context</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="398" 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="418" 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">@@ -398,6 +418,7 @@ struct MethylDcmAlphabet : public Alphabet</td>
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398
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Global alphabet objects that can be re-used</span></span>
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399
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">DNAAlphabet</span> <span class="n" style="color: #333;">gDNAAlphabet</span><span class="p">;</span></span>
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">MethylCpGAlphabet</span> <span class="n" style="color: #333;">gMCpGAlphabet</span><span class="p">;</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">MethylGpCAlphabet</span> <span class="n" style="color: #333;">gMethylGpCAlphabet</span><span class="p">;</span></span>
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401
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">MethylDamAlphabet</span> <span class="n" style="color: #333;">gMethylDamAlphabet</span><span class="p">;</span></span>
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402
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">MethylDcmAlphabet</span> <span class="n" style="color: #333;">gMethylDcmAlphabet</span><span class="p">;</span></span>
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403
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">UtoTRNAAlphabet</span> <span class="n" style="color: #333;">gUtoTRNAAlphabet</span><span class="p">;</span></span>
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<li id="58a43c64ead5187f569b28ec5ca98b313c48d7c7">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#58a43c64ead5187f569b28ec5ca98b313c48d7c7"><strong>src/common/nanopolish_common.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">@@ -18,7 +18,7 @@</td>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "logsum.h"</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_NAME "nanopolish"</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.1<span class="idiff left right">0.2</span>"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.1<span class="idiff left right">1.0</span>"</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_BUGREPORT "https://github.com/jts/nanopolish/issues"</span></span>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#af0c7b92cdf7a0cc7d98c3103b7fba80623a54e1"><strong>src/common/nanopolish_fast5_io.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">@@ -8,65 +8,91 @@</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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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 <string.h></span></span>
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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 <math.h></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_fast5_io.h"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define DEBUG_FAST5_IO 1</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define RAW_ROOT "/Raw/Reads/"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define LEGACY_FAST5_RAW_ROOT "/Raw/Reads/"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</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="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left right">hid_t</span></span> <span class="nf" style="color: #900; font-weight: 600;">fast5_open</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left right">fast5_file</span></span> <span class="nf" style="color: #900; font-weight: 600;">fast5_open</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5F_ACC_RDONLY</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hdf5file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_file</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5F_ACC_RDONLY</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check for attribute that indicates whether it is single or multi-fast5</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// see: https://community.nanoporetech.com/posts/multi-fast5-format</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">indicator_p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/UniqueGlobalKey/"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">indicator_p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indicator_p1</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"tracking_id/"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_indicator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Lexists</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">indicator_p1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">H5Lexists</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">indicator_p2</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">has_indicator</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fh</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">fast5_close</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">fast5_is_open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fh</span></span><span class="p">)</span></span>
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27
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">H5Fclose</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hdf5_file</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">hdf5_file</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fast5_get_raw_read_group</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">fast5_close</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fh</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_read_name</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</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;">RAW_ROOT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_name</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Fclose</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fast5_get_raw_read_name</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fast5_get_multi_read_groups</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fh</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This code is From scrappie's fast5_interface</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// retrieve the size of the read name</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">ssize_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Lget_name_by_idx</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">RAW_ROOT</span><span class="p">,</span> <span class="n" style="color: #333;">H5_INDEX_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">H5_ITER_INC</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">buffer_size</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="LC52" class="line" lang="cpp"> <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;">buffer</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="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get the number of groups in the root group</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">H5G_info_t</span> <span class="n" style="color: #333;">group_info</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Gget_info_by_name</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"/"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">group_info</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error getting group info</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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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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54
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="p">}</span></span>
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61
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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="LC56" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// copy the read name out of the fast5</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <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;">name</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Lget_name_by_idx</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">RAW_ROOT</span><span class="p">,</span> <span class="n" style="color: #333;">H5_INDEX_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">H5_ITER_INC</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="mi" style="color: #099;">1</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;">H5P_DEFAULT</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" 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;">size_t</span> <span class="n" style="color: #333;">group_idx</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;">group_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">group_info</span><span class="p">.</span><span class="n" style="color: #333;">nlinks</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">group_idx</span><span class="p">)</span> <span class="p">{</span></span>
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63
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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="c1" style="color: #998; font-style: italic;">// retrieve the size of this group name</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">ssize_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Lget_name_by_idx</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"/"</span><span class="p">,</span> <span class="n" style="color: #333;">H5_INDEX_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">H5_ITER_INC</span><span class="p">,</span> <span class="n" style="color: #333;">group_idx</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error getting group name size</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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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// for null terminator</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">buffer_size</span><span class="p">)</span> <span class="p">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</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;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// copy the group name</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Lget_name_by_idx</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"/"</span><span class="p">,</span> <span class="n" style="color: #333;">H5_INDEX_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">H5_ITER_INC</span><span class="p">,</span> <span class="n" style="color: #333;">group_idx</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</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="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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60
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// cleanup</span></span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">out</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">free</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">free</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff right">);</span></span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">buffer</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">buffer_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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64
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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65
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"><span class="p">}</span></span>
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66
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"></span>
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67
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_read_id</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_read_id<span class="idiff left">_single_fast5</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fh</span></span><span class="p">)</span></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this function is not supported for multi-fast5 files</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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71
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">read_name_attribute</span><span class="p">,</span> <span class="n" style="color: #333;">raw_group</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_type</span><span class="p">;</span></span>
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72
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">storage_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,16 +101,16 @@ std::string fast5_get_read_id(hid_t hdf5_file)</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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76
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get the path to the raw read group</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">raw_read_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hdf5_file</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">raw_read_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">raw_read_group</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"></span>
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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;">return</span> <span class="n" style="color: #333;">fast5_get_<span class="idiff left">fixed_string_attribute</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">,</span> <span class="n" style="color: #333;">raw_read_group</span><span class="p">,</span> <span class="s" style="color: #d14;">"read_id"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fast5_get_<span class="idiff left">string_attribute</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fh</span></span><span class="p">,</span> <span class="n" style="color: #333;">raw_read_group</span><span class="p">,</span> <span class="s" style="color: #d14;">"read_id"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">fast5_get_raw_samples</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">,</span> <span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">scaling</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">fast5_get_raw_samples</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">,</span> <span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">scaling</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rawptr</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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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">space</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" 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="120" 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">@@ -94,12 +120,12 @@ raw_table fast5_get_raw_samples(hid_t hdf5_file, fast5_raw_scaling scaling)</td>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">rawtbl</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">};</span></span>
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// mostly from scrappie</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">raw_read_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hdf5_file</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">raw_read_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Create data set name</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">signal_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_read_group</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/Signal"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">dset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Dopen</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">signal_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">dset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Dopen</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fh</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">signal_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_FAST5_IO</span></span>
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105
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failed to open dataset '%s' to read raw signal from.</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;">signal_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,12 +166,27 @@ raw_table fast5_get_raw_samples(hid_t hdf5_file, fast5_raw_scaling scaling)</td>
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140
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rawtbl</span><span class="p">;</span></span>
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141
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"><span class="p">}</span></span>
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142
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_context_tags_group</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_id</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"><span class="p">{</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"/read_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/context_tags"</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"/UniqueGlobalKey/context_tags"</span><span class="p">;</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">group</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"></span>
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_<span class="idiff left">experiment_type</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_<span class="idiff left">sequencing_kit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">)</span></span>
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145
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"><span class="p">{</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fast5_get_fixed_string_attribute</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"/UniqueGlobalKey/context_tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"experiment_type"</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_context_tags_group</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="n" style="color: #333;">read_id</span><span class="p">);</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fast5_get_string_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"sequencing_kit"</span><span class="p">);</span></span>
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147
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"><span class="p">}</span></span>
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148
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_experiment_type</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_id</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"><span class="p">{</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_context_tags_group</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="n" style="color: #333;">read_id</span><span class="p">);</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fast5_get_string_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"experiment_type"</span><span class="p">);</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"><span class="p">}</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"></span>
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149
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// from scrappie</span></span>
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150
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fast5_read_float_attribute</span><span class="p">(</span><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">attribute</span><span class="p">)</span> <span class="p">{</span></span>
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151
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" 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="212" 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">@@ -171,16 +212,18 @@ float fast5_read_float_attribute(hid_t group, const char *attribute) {</td>
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171
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"><span class="p">}</span></span>
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172
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"></span>
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173
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"><span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">fast5_get_channel_params</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"><span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">fast5_get_channel_params</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">)</span></span>
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175
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"><span class="p">{</span></span>
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176
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// from scrappie</span></span>
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177
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">scaling</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="n" style="color: #333;">NAN</span><span class="p">,</span> <span class="n" style="color: #333;">NAN</span><span class="p">,</span> <span class="n" style="color: #333;">NAN</span><span class="p">,</span> <span class="n" style="color: #333;">NAN</span> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scaling_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/UniqueGlobalKey/channel_id"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">scaling_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Gopen</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">scaling_path</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">scaling_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"/read_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/channel_id"</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"/UniqueGlobalKey/channel_id"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">scaling_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Gopen</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">scaling_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scaling_group</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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182
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_FAST5_IO</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failed to <span class="idiff left">group %s."</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">scaling_path</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failed to <span class="idiff left">open group %s</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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">scaling_path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC227" 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="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">scaling</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -200,23 +243,61 @@ fast5_raw_scaling fast5_get_channel_params(hid_t hdf5_file)</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_<span class="idiff left">fixed_string_attribute</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hdf5_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">group_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">attribute_name</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_<span class="idiff left">raw_root</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">storage_size</span><span class="p">;</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <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;">buffer</span><span class="p">;</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">attribute</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_type</span><span class="p">;</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"/read_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/Raw"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"/Raw/Reads"</span><span class="p">;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_id</span><span class="p">)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"><span class="p">{</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"/read_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/Raw"</span><span class="p">;</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">internal_read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_read_internal_name</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">);</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">internal_read_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</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;">string</span><span class="p">(</span><span class="n" style="color: #333;">LEGACY_FAST5_RAW_ROOT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">internal_read_name</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="p">}</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"><span class="p">}</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_raw_read_internal_name</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">)</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"><span class="p">{</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This code is From scrappie's fast5_interface</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// retrieve the size of the read name</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">ssize_t</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Lget_name_by_idx</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">LEGACY_FAST5_RAW_ROOT</span><span class="p">,</span> <span class="n" style="color: #333;">H5_INDEX_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">H5_ITER_INC</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="p">}</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// copy the read name out of the fast5</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <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;">name</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Lget_name_by_idx</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">LEGACY_FAST5_RAW_ROOT</span><span class="p">,</span> <span class="n" style="color: #333;">H5_INDEX_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">H5_ITER_INC</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cleanup</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"><span class="p">}</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_string_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">group_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">attribute_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"><span class="p">{</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">attribute</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_type</span><span class="p">,</span> <span class="n" style="color: #333;">native_type</span><span class="p">;</span></span>
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209
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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210
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>
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211
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// according to http://hdf-forum.184993.n3.nabble.com/check-if-dataset-exists-td194725.html</span></span>
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212
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we should use H5Lexists to check for the existence of a group/dataset using an arbitrary path</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Lexists</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// HDF5 1.8 returns 0 on the root group, so we explicitly check for it</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">H5Lexists</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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214
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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215
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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216
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="p">}</span></span>
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217
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open the group <span class="idiff left right">/Raw/Reads/Read_nnn</span></span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Gopen</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open the group <span class="idiff left right">containing the attribute we want</span></span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Gopen</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fh</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>
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220
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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221
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_FAST5_IO</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"could not open group %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -241,25 +322,61 @@ std::string fast5_get_fixed_string_attribute(hid_t hdf5_file, const std::string&</td>
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241
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"></span>
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242
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get data type and check it is a fixed-length string</span></span>
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243
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">attribute_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Aget_type</span><span class="p">(</span><span class="n" style="color: #333;">attribute</span><span class="p">);</span></span>
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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">H5Tis_variable_str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">attribute_type</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">attribute_type</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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245
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_FAST5_IO</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">variable length string detected -- ignoring attribute</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">failed to get attribute type %s</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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">attribute_name</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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247
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<pre style="margin: 0;"> <span id="LC328" 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="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">close_type</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get the storage size and allocate</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">storage_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Aget_storage_size</span><span class="p">(</span><span class="n" style="color: #333;">attribute</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</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;">storage_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">H5Tget_class</span><span class="p">(</span><span class="n" style="color: #333;">attribute_type</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">H5T_STRING</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_FAST5_IO</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"attribute %s is not a string</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;">attribute_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC335" 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="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">close_type</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="p">}</span></span>
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254
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// finally read the attribute</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Aread</span><span class="p">(</span><span class="n" style="color: #333;">attribute</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_type</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">native_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Tget_native_type</span><span class="p">(</span><span class="n" style="color: #333;">attribute_type</span><span class="p">,</span> <span class="n" style="color: #333;">H5T_DIR_ASCEND</span><span class="p">);</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">native_type</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_FAST5_IO</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"failed to get native type for %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">close_native_type</span><span class="p">;</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="p">}</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">H5Tis_variable_str</span><span class="p">(</span><span class="n" style="color: #333;">attribute_type</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// variable length string</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <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;">buffer</span><span class="p">;</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Aread</span><span class="p">(</span><span class="n" style="color: #333;">attribute</span><span class="p">,</span> <span class="n" style="color: #333;">native_type</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="351" 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">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error reading attribute %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="p">}</span></span>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer</span><span class="p">;</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</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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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fixed length string</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">storage_size</span><span class="p">;</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <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;">buffer</span><span class="p">;</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get the storage size and allocate</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">storage_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Aget_storage_size</span><span class="p">(</span><span class="n" style="color: #333;">attribute</span><span class="p">);</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</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;">storage_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// finally read the attribute</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Aread</span><span class="p">(</span><span class="n" style="color: #333;">attribute</span><span class="p">,</span> <span class="n" style="color: #333;">attribute_type</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="p">}</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// clean up</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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259
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// clean up</span></span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">free</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff right">);</span></span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">close_native_type</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">:</span></span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">H5Tclose</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">native_type</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff right"> </span></span>
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263
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"><span class="n" style="color: #333;">close_type</span><span class="o" style="font-weight: 600;">:</span></span>
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264
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">H5Tclose</span><span class="p">(</span><span class="n" style="color: #333;">attribute_type</span><span class="p">);</span></span>
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265
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"><span class="n" style="color: #333;">close_attr</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" 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="386" 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">@@ -269,4 +386,3 @@ close_group:</td>
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269
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"></span>
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270
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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271
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"><span class="p">}</span></span></pre>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"></span></pre>
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<li id="a6b650afca4ceb444770725cd6e17939daeec862">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#a6b650afca4ceb444770725cd6e17939daeec862"><strong>src/common/nanopolish_fast5_io.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">@@ -21,45 +21,75 @@ extern "C" {</td>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// From scrappie</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right"> Information</span> for scaling raw data from ADC values to pA</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Parameters</span> for scaling raw data from ADC values to pA</span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">digitisation</span><span class="p">;</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">range</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">sample_rate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">fast5_raw_scaling</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">fast5_file</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5_file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">is_multi_fast5</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// External API</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// open the file and return the hdf ID</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Basic I/O</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// open the file and return handle</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"><span class="n" style="color: #333;">fast5_file</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// check if file is open</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">fast5_is_open</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// close the file</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fast5_close</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fast5_close</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fh</span></span><span class="p">);</span></span>
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41
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// get the raw samples from this file</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"><span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">fast5_get_raw_samples</span><span class="p">(</span><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">scaling</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Functions to get the names of the read(s) contained in the file</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// get the name of the raw read in the file (eg Read_1234)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_raw_read_name</span><span class="p">(</span><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Get the identifier of a read from the hdf5 file (eg 00041f-....)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_read_id_single_fast5</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Get a vector of read groups for a multi-fast5 file (eg [read_00041f-..., read_1243fe-....])</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fast5_get_multi_read_groups</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// get the name of the raw read group (eg /Raw/Read/Read_1234)</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Functions to get the samples or metadata</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Get the identifier of a read from the hdf5 file</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_read_id</span><span class="p">(</span><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// get the raw samples from this file</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">fast5_get_raw_samples</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">scaling</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Get the sequencing kit</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_sequencing_kit</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_id</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Get the experiment type attribute</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_experiment_type</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_experiment_type</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Get sample rate, and ADC-to-pA scalings</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">fast5_get_channel_params</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hdf5_file</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="n" style="color: #333;">fast5_raw_scaling</span> <span class="n" style="color: #333;">fast5_get_channel_params</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_id</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Internal utility functions</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_fixed_string_attribute</span><span class="p">(</span><span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">hdf5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">group_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">attribute_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// get the name of the raw read in the file (eg Read_1234)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_raw_read_internal_name</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// get the name of the raw read group (eg /Raw/Read/Read_1234 or /read_00041f-.../Raw/)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_raw_read_group</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_id</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fast5_get_string_attribute</span><span class="p">(</span><span class="n" style="color: #333;">fast5_file</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">group_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">attribute_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<li id="149ac5b0310ff017664f0645808befe6bda2ed83">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#149ac5b0310ff017664f0645808befe6bda2ed83"><strong>src/common/nanopolish_variant.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">@@ -391,7 +391,13 @@ std::vector<Variant> simple_call(VariantGroup& variant_group,</td>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">add_info</span><span class="p">(</span><span class="s" style="color: #d14;">"TotalReads"</span><span class="p">,</span> <span class="n" style="color: #333;">group_reads</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">add_info</span><span class="p">(</span><span class="s" style="color: #d14;">"AlleleCount"</span><span class="p">,</span> <span class="n" style="color: #333;">var_count</span><span class="p">);</span></span>
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393
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">add_info</span><span class="p">(</span><span class="s" style="color: #d14;">"SupportFraction"</span><span class="p">,</span> <span class="n" style="color: #333;">read_variant_support</span><span class="p">[</span><span class="n" style="color: #333;">vi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">group_reads</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_genotype</span><span class="p">(</span><span class="n" style="color: #333;">var_count</span><span class="p">,</span> <span class="n" style="color: #333;">ploidy</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">group_reads</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_genotype</span><span class="p">(</span><span class="n" style="color: #333;">var_count</span><span class="p">,</span> <span class="n" style="color: #333;">ploidy</span><span class="p">);</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"></span>
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">output_variants</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"> <span class="p">}</span></span>
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"></span>
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<li id="125985123a25635dc9e1a81a7b2849a0f12aa286">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#125985123a25635dc9e1a81a7b2849a0f12aa286"><strong>src/nanopolish_call_methylation.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +98,7 @@ static const char *CALL_METHYLATION_USAGE_MESSAGE =</td>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="s" style="color: #d14;">" -r, --reads=FILE the ONT reads are in fasta FILE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="s" style="color: #d14;">" -b, --bam=FILE the reads aligned to the genome assembly are in bam FILE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="s" style="color: #d14;">" -g, --genome=FILE the genome we are computing a consensus for is in FILE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"><span class="s" style="color: #d14;">" -q, --methylation=STRING the type of methylation (cpg,dam,dcm)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="s" style="color: #d14;">" -q, --methylation=STRING the type of methylation (cpg,<span class="idiff left right">gpc,</span>dam,dcm)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="s" style="color: #d14;">" -t, --threads=NUM use NUM threads (default: 1)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"><span class="s" style="color: #d14;">" --progress print out a progress message</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"><span class="s" style="color: #d14;">" -K --batchsize=NUM the batch size (default: 512)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#2d62e059707d17d6d88d86a4af4fce9c4c482e3d"><strong>src/nanopolish_index.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">@@ -55,6 +55,7 @@ namespace opt</td>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">os_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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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_file_from_map</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</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;">string</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">PROFILE_FUNC</span><span class="p">(</span><span class="s" style="color: #d14;">"index_file_from_map"</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,24 +74,38 @@ void index_file_from_map(ReadDB& read_db, const std::string& fn, const std::map<</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Could not find read %s in sequencing summary file</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;">fn</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="p">}</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// process_file</span></span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_file_from_fast5</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</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;">string</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">PROFILE_FUNC</span><span class="p">(</span><span class="s" style="color: #d14;">"index_file_from_fast5"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hd</span>f5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hdf5_file</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></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="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">f5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_is_open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f5_file</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"could not open fast5 file: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_read_id</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">add_signal_path</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">.</span><span class="n" style="color: #333;">is_multi_fast5</span><span class="p">)</span> <span class="p">{</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">read_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_multi_read_groups</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"read_"</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" 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;">size_t</span> <span class="n" style="color: #333;">group_idx</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;">group_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">read_groups</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="n" style="color: #333;">group_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">group_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_groups</span><span class="p">[</span><span class="n" style="color: #333;">group_idx</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_name</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">add_signal_path</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="p">}</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_read_id_single_fast5</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">);</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">add_signal_path</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="p">}</span></span>
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90
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="p">}</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_close</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hd</span>f5_file</span><span class="p">);</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"><span class="p">}</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// process_file</span></span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_close</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"><span class="p">}</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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94
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_path</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</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;">string</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">)</span></span>
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95
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"><span class="p">{</span></span>
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96
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[readdb] indexing %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" 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="129" 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">@@ -114,7 +129,7 @@ void index_path(ReadDB& read_db, const std::string& path, const std::map<std::st</td>
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114
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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115
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="p">}</span></span>
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116
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="p">}</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"><span class="p">}</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// process_path</span></span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"><span class="p">}</span></span>
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118
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="119" 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">
119
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// read sequencing summary files from the fofn and add them to the list</span></span>
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<td class="diff-line-num old_line" data-linenumber="120" 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">
120
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">process_summary_fofn</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,6 +152,7 @@ void process_summary_fofn()</td>
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137
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="138" 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">
138
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"><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="c1" style="color: #998; font-style: italic;">//</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">exit_bad_header</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"><span class="p">{</span></span>
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142
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Could not find %s column in the header of %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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="164" 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">@@ -148,8 +164,8 @@ void parse_sequencing_summary(const std::string& filename, std::map<std::string,</td>
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<td class="diff-line-num old_line" data-linenumber="148" 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">
148
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"><span class="p">{</span></span>
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149
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// open</span></span>
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150
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">in_file</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">in_file</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ba</span>d</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error: could not file %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">in_file</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">goo</span>d</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error: could not <span class="idiff left right">read </span>file %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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153
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<td class="diff-line-num new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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154
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="p">}</span></span>
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155
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="261" 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="277" 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">@@ -261,7 +277,6 @@ int index_main(int argc, char** argv)</td>
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261
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_index_options</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read a map from fast5 files to read name from the sequencing summary files (if any)</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">process_summary_fofn</span><span class="p">();</span></span>
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267
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</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;">string</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">;</span></span>
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<li id="9e1d6734082431b228580bb425603ab97d4c9d1d">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#9e1d6734082431b228580bb425603ab97d4c9d1d"><strong>src/nanopolish_methyltrain.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">@@ -23,6 +23,9 @@</td>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <omp.h></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <getopt.h></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstddef></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <functional></span></span>
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28
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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 <unordered_map></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "htslib/faidx.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_methyltrain.h"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_eventalign.h"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,6 +115,7 @@ static const char *METHYLTRAIN_USAGE_MESSAGE =</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="s" style="color: #d14;">" --max-reads=NUM stop after processing NUM reads in each round</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="s" style="color: #d14;">" --progress print out a progress message</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="s" style="color: #d14;">" --stdv enable stdv modelling</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"><span class="s" style="color: #d14;">" --max-events=NUM use NUM events for training (default: 1000)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Report bugs to "</span> <span class="n" style="color: #333;">PACKAGE_BUGREPORT</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">opt</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" 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="145" 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">@@ -141,6 +145,7 @@ namespace opt</td>
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141
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">min_distance_from_alignment_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">min_number_of_events_to_train</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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143
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">num_training_rounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">max_events</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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144
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"><span class="p">}</span></span>
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145
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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146
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<td class="diff-line-num new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;"> <span id="LC151" 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;">shortopts</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"r:b:g:t:m:vnc"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" 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="165" 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">@@ -160,7 +165,8 @@ enum { OPT_HELP = 1,</td>
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160
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_P_SKIP_SELF</span><span class="p">,</span></span>
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161
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_P_BAD</span><span class="p">,</span></span>
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162
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_P_BAD_SELF</span><span class="p">,</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_MAX_READS</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_MAX_READS</span><span class="p">,</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_MAX_EVENTS</span></span>
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164
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="p">};</span></span>
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165
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>
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166
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">longopts</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="188" 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="194" 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">@@ -188,6 +194,7 @@ static const struct option longopts[] = {</td>
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188
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"filter-policy"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_FILTER_POLICY</span> <span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="189" 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">
189
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"rounds"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_NUM_ROUNDS</span> <span class="p">},</span></span>
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190
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"max-reads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MAX_READS</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"max-events"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_MAX_EVENTS</span> <span class="p">},</span></span>
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191
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="p">{</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">}</span></span>
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192
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC200" 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">@@ -299,6 +306,25 @@ bool recalibrate_model(SquiggleRead &sr,</td>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">recalibrated</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Use reservoir sampling to limit the amount of events for each kmer</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">add_event</span><span class="p">(</span><span class="n" style="color: #333;">StateSummary</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kmer_summary</span><span class="p">,</span> <span class="n" style="color: #333;">StateTrainingData</span> <span class="n" style="color: #333;">std</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">event_count</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add all events for each kmer until we have the maximum number of events to train</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">event_count</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max_events</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 class="n" style="color: #333;">kmer_summary</span><span class="p">.</span><span class="n" style="color: #333;">events</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Select a random number between 0 and the total number of events for this kmer</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mt19937</span> <span class="n" style="color: #333;">rng</span><span class="p">(</span><span class="n" style="color: #333;">event_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gen</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">event_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rs_location</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gen</span><span class="p">(</span><span class="n" style="color: #333;">rng</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Only update the training data if the random number is below the maximum number of events</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rs_location</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max_events</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">kmer_summary</span><span class="p">.</span><span class="n" style="color: #333;">events</span><span class="p">[</span><span class="n" style="color: #333;">rs_location</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Update the training data with aligned events from a read</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">add_aligned_events</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span></span>
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fai</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -311,7 +337,8 @@ void add_aligned_events(const ReadDB& read_db,</td>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">training_alphabet</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">training_k</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">round</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">ModelTrainingMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">training</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">ModelTrainingMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">training</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">event_count</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Load a squiggle read for the mapped read</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -429,7 +456,10 @@ void add_aligned_events(const ReadDB& read_db,</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">use_for_training</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">StateTrainingData</span> <span class="n" style="color: #333;">std</span><span class="p">(</span><span class="n" style="color: #333;">sr</span><span class="p">,</span> <span class="n" style="color: #333;">ea</span><span class="p">,</span> <span class="n" style="color: #333;">rank</span><span class="p">,</span> <span class="n" style="color: #333;">prev_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">next_kmer</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma omp critical(kmer)</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">kmer_summary</span><span class="p">.</span><span class="n" style="color: #333;">events</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">event_count</span><span class="p">[</span><span class="n" style="color: #333;">rank</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">add_event</span><span class="p">(</span><span class="n" style="color: #333;">kmer_summary</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="p">,</span> <span class="n" style="color: #333;">event_count</span><span class="p">[</span><span class="n" style="color: #333;">rank</span><span class="p">]);</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="p">}</span></span>
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463
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"> <span class="p">}</span></span>
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434
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464
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"></span>
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435
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465
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ea</span><span class="p">.</span><span class="n" style="color: #333;">hmm_state</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="473" 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="503" 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">@@ -473,6 +503,7 @@ void parse_methyltrain_options(int argc, char** argv)</td>
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473
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_P_BAD</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">g_p_bad</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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474
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<td class="diff-line-num new_line" data-linenumber="504" 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">
504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_P_BAD_SELF</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">g_p_bad_self</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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475
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_MAX_READS</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max_reads</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_MAX_EVENTS</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max_events</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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476
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_HELP</span><span class="p">:</span></span>
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477
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">METHYLTRAIN_USAGE_MESSAGE</span><span class="p">;</span></span>
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478
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="755" 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="786" 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">@@ -755,6 +786,7 @@ void train_one_round(const ReadDB& read_db,</td>
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755
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">num_reads_realigned</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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756
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">num_records_buffered</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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757
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">Progress</span> <span class="n" style="color: #333;">progress</span><span class="p">(</span><span class="s" style="color: #d14;">"[methyltrain]"</span><span class="p">);</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">event_count</span><span class="p">;</span></span>
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758
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="cpp"></span>
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759
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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760
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">num_records_buffered</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">records</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -773,7 +805,7 @@ void train_one_round(const ReadDB& read_db,</td>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="cpp"> <span class="n" style="color: #333;">add_aligned_events</span><span class="p">(</span><span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="n" style="color: #333;">fai</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">,</span> <span class="n" style="color: #333;">read_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="cpp"> <span class="n" style="color: #333;">clip_start</span><span class="p">,</span> <span class="n" style="color: #333;">clip_end</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="cpp"> <span class="n" style="color: #333;">kit_name</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="cpp"> <span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="n" style="color: #333;">model_training_data</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="cpp"> <span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="n" style="color: #333;">model_training_data</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">event_count</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#a9c87dc87f669219ca843a7b27aba683ef12b563"><strong>src/nanopolish_raw_loader.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">@@ -69,6 +69,11 @@ SquiggleScalings estimate_scalings_using_mom(const std::string& sequence,</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define move_down(curr_band) { curr_band.event_idx + 1, curr_band.kmer_idx }</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define move_right(curr_band) { curr_band.event_idx, curr_band.kmer_idx + 1 }</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define ALN_BANDWIDTH 100</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define BAND_ARRAY(r, c) ( bands[((r)*(ALN_BANDWIDTH)+(c))] )</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define TRACE_ARRAY(r, c) ( trace[((r)*(ALN_BANDWIDTH)+(c))] )</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignedPair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">adaptive_banded_simple_event_align</span><span class="p">(</span><span class="n" style="color: #333;">SquiggleRead</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PoreModel</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pore_model</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">strand_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" 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="92" 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">@@ -87,7 +92,7 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_gap_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// banding</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">ALN_BANDWIDTH</span></span><span class="p">;</span></span>
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91
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">half_bandwidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bandwidth</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// transition penalties</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -115,15 +120,21 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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115
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">kmer_ranks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_rank</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">k</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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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bandscore</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bandtrace</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bandscore</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bands</span><span class="p">(</span><span class="n" style="color: #333;">n_bands</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bandtrace</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trace</span><span class="p">(</span><span class="n" style="color: #333;">n_bands</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC124" 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;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_bands</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">bands</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">trace</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">bandwidth</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bands</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="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n_bands</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bandwidth</span><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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bands</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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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Memory allocation failed at %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">__func__</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">trace</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n_bands</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">);</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">trace</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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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Memory allocation failed at %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">__func__</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" 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;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_bands</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" 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;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">BAND_ARRAY</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</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="n" style="color: #333;">TRACE_ARRAY</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="p">}</span></span>
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127
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="p">}</span></span>
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128
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>
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129
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Keep track of the event/kmer index for the lower left corner of the band</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" 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="157" 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">@@ -146,18 +157,18 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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146
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start_cell_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_kmer_to_offset</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">start_cell_offset</span><span class="p">));</span></span>
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148
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">band_event_to_offset</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">start_cell_offset</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">start_cell_offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">start_cell_offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"></span>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// band 1: first event is trimmed</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">first_trim_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_event_to_offset</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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153
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">kmer_at_offset</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">first_trim_offset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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154
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">first_trim_offset</span><span class="p">));</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">first_trim_offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lp_trim</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">trace</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">first_trim_offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FROM_U</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">first_trim_offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lp_trim</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">TRACE_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">first_trim_offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FROM_U</span><span class="p">;</span></span>
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157
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>
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158
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fills</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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159
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_ADAPTIVE</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[trim] bi: %d o: %d e: %d k: %d s: %.2lf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">first_trim_offset</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">first_trim_offset</span></span><span class="p"><span class="idiff right">]</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[trim] bi: %d o: %d e: %d k: %d s: %.2lf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">first_trim_offset</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">first_trim_offset</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC172" 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="LC173" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fill in remaining bands</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">@@ -165,11 +176,11 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Determine placement of this band according to Suzuki's adaptive algorithm</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// When both ll and ur are out-of-band (ob) we alternate movements</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// otherwise we decide based on scores</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">ur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">bandwidth</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">ur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">bandwidth</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ll_ob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ur_ob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ur</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">right</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ll_ob</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ur_ob</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">right</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_idx</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="217" 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">@@ -206,10 +217,10 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">trim_offset</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">event_at_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span><span class="p">,</span> <span class="n" style="color: #333;">trim_offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_events</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">trim_offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lp_trim</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">trace</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">trim_offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FROM_U</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">trim_offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lp_trim</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">event_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">TRACE_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">trim_offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FROM_U</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">trim_offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">trim_offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC226" 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">@@ -231,11 +242,11 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmer_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_at_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">kmer_rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_ranks</span><span class="p">[</span><span class="n" style="color: #333;">kmer_idx</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset_up</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_event_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</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;">event_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset_up</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_event_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</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;">event_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_kmer_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</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;">kmer_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_kmer_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_ADAPTIVE</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// verify loop conditions</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">kmer_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">kmer_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_kmers</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -245,10 +256,10 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bandwidth</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC257" 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="LC258" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">up</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset_up</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset_up</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset_left</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset_left</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset_diag</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset_diag</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">up</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset_up</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset_up</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset_left</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset_left</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset_diag</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset_diag</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"></span>
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252
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<td class="diff-line-num new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">lp_emission</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_probability_match_r9</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">pore_model</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_rank</span><span class="p">,</span> <span class="n" style="color: #333;">event_idx</span><span class="p">,</span> <span class="n" style="color: #333;">strand_idx</span><span class="p">);</span></span>
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253
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">score_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diag</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lp_step</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lp_emission</span><span class="p">;</span></span>
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254
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<td class="diff-line-num new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">score_u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">up</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lp_stay</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lp_emission</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="261" 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="272" 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">@@ -261,18 +272,18 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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261
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score_u</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">FROM_U</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">from</span><span class="p">;</span></span>
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262
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score_l</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">score_l</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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263
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score_l</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">FROM_L</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">from</span><span class="p">;</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"></span>
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265
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_ADAPTIVE</span></span>
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266
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[adafill] offset-up: %d offset-diag: %d offset-left: %d</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;">offset_up</span><span class="p">,</span> <span class="n" style="color: #333;">offset_diag</span><span class="p">,</span> <span class="n" style="color: #333;">offset_left</span><span class="p">);</span></span>
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267
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[adafill] up: %.2lf diag: %.2lf left: %.2lf</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;">up</span><span class="p">,</span> <span class="n" style="color: #333;">diag</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="p">);</span></span>
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268
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<td class="diff-line-num new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[adafill] bi: %d o: %d e: %d k: %d s: %.2lf f: %d emit: %.2lf</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;">band_idx</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">event_idx</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_idx</span><span class="p">,</span> <span class="n" style="color: #333;">max_score</span><span class="p">,</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="n" style="color: #333;">lp_emission</span><span class="p">);</span></span>
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269
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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270
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<td class="diff-line-num new_line old" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">trace</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_score</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">TRACE_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span></span>
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272
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">fills</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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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="p">}</span></span>
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC287" 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="LC288" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // Debug, print some of the score matrix</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for(int col = 0; col <= 10; ++col) {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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="305" 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">@@ -294,7 +305,7 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum_emission</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="LC306" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">n_aligned_events</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="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignedPair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"></span>
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298
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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299
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">curr_event_idx</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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300
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">curr_kmer_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_kmers</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="302" 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="313" 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">@@ -302,17 +313,16 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find best score between an event and the last k-mer. after trimming the remaining evnets</span></span>
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<pre style="margin: 0;"> <span id="LC314" 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;">event_idx</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;">event_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_events</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">event_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">band_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">event_kmer_to_band</span><span class="p">(</span><span class="n" style="color: #333;">event_idx</span><span class="p">,</span> <span class="n" style="color: #333;">curr_kmer_idx</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bands</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_event_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span><span class="p">,</span> <span class="n" style="color: #333;">event_idx</span><span class="p">);</span></span>
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307
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">is_offset_valid</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">))</span> <span class="p">{</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">bands</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">n_events</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">event_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lp_trim</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">BAND_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">n_events</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">event_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lp_trim</span><span class="p">;</span></span>
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309
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">curr_event_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">event_idx</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_ADAPTIVE</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[adaback] ei: %d ki: %d s: %.2f</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;">curr_event_idx</span><span class="p">,</span> <span class="n" style="color: #333;">curr_kmer_idx</span><span class="p">,</span> <span class="n" style="color: #333;">max_score</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -320,12 +330,12 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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320
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">curr_gap</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="LC331" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_gap</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="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">curr_kmer_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">curr_event_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// emit alignment</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">curr_kmer_idx</span><span class="p">,</span> <span class="n" style="color: #333;">curr_event_idx</span><span class="p">});</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG_ADAPTIVE</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[adaback] ei: %d ki: %d</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;">curr_event_idx</span><span class="p">,</span> <span class="n" style="color: #333;">curr_kmer_idx</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC338" 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="LC339" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// qc stats</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">kmer_rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_rank</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">curr_kmer_idx</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_emission</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">log_probability_match_r9</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">pore_model</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_rank</span><span class="p">,</span> <span class="n" style="color: #333;">curr_event_idx</span><span class="p">,</span> <span class="n" style="color: #333;">strand_idx</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -335,7 +345,7 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band_event_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span><span class="p">,</span> <span class="n" style="color: #333;">curr_event_idx</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">band_kmer_to_offset</span><span class="p">(</span><span class="n" style="color: #333;">band_idx</span><span class="p">,</span> <span class="n" style="color: #333;">curr_kmer_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">trace</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">TRACE_ARRAY</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">band_idx</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FROM_D</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">curr_kmer_idx</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">curr_event_idx</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -347,7 +357,7 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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347
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">curr_kmer_idx</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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348
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">curr_gap</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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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">max_gap</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;">max</span><span class="p">(</span><span class="n" style="color: #333;">curr_gap</span><span class="p">,</span> <span class="n" style="color: #333;">max_gap</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"> <span class="p">}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="371" 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">@@ -361,6 +371,9 @@ std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,</td>
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361
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bands</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">trace</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "ada\t%s\t%s\t%.2lf\t%zu\t%.2lf\t%d\t%d\t%d\n", read.read_name.substr(0, 6).c_str(), failed ? "FAILED" : "OK", events_per_kmer, sequence.size(), avg_log_emission, curr_event_idx, max_gap, fills);</span></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#7c87ffe15195ab460f3be130ef4d8324408853f0"><strong>src/nanopolish_read_db.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">@@ -139,7 +139,7 @@ void ReadDB::import_reads(const std::string& input_filename, const std::string&</td>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// as a sanity check we require the path name to end in ".fast5"</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">".fast5"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">length</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">".fast5"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="244f2077b9e28a5e6394deda0b7574b0f80f501c">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#244f2077b9e28a5e6394deda0b7574b0f80f501c"><strong>src/nanopolish_squiggle_read.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">@@ -82,17 +82,17 @@ SquiggleRead::SquiggleRead(const std::string& name, const ReadDB& read_db, const</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></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="LC85" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get the read type from the fast5 file</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hd</span>f5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="n" style="color: #333;">fast5_path</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hdf5_file</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">f5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="n" style="color: #333;">fast5_path</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_is_open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f5_file</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "file: %s\n", fast5_path.c_str());</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">experiment_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_experiment_type</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "type: %s\n", experiment_type.c_str());</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sequencing_kit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_sequencing_kit</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">experiment_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_experiment_type</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Try to detect whether this read is DNA or RNA</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nucleotide_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">experiment_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rna"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">experiment_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"internal_rna"</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">SRNT_RNA</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SRNT_DNA</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fix issue 531: experiment_type in fast5 is "rna" for cDNA kit dcs108</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rna_experiment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">experiment_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rna"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">experiment_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"internal_rna"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nucleotide_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rna_experiment</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequencing_kit</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"sqk-dcs108"</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">SRNT_RNA</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SRNT_DNA</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Did this read come from nanopolish extract?</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_event_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_extract_read_name</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -115,10 +115,10 @@ SquiggleRead::SquiggleRead(const std::string& name, const ReadDB& read_db, const</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">f_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">get_read_sequence</span><span class="p">(</span><span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">load_from_raw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hd</span>f5_file</span><span class="p">,</span> <span class="n" style="color: #333;">flags</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">load_from_raw</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">,</span> <span class="n" style="color: #333;">flags</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_close</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hd</span>f5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_close</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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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;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[warning] fast5 file is unreadable and will be skipped: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fast5_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -271,7 +271,7 @@ void SquiggleRead::load_from_events(const uint32_t flags)</td>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SquiggleRead</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load_from_raw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hd</span>f5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SquiggleRead</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load_from_raw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">f5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// File not in db, can't load</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fast5_path</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" 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="304" 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">@@ -304,11 +304,11 @@ void SquiggleRead::load_from_raw(hid_t hdf5_file, const uint32_t flags)</td>
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">base_model</span><span class="p">[</span><span class="n" style="color: #333;">strand_idx</span><span class="p">]</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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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read the sample rate</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">channel_params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_channel_params</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hdf5_fil</span>e</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">channel_params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_channel_params</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">f5_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">read_nam</span>e</span><span class="p">);</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">channel_params</span><span class="p">.</span><span class="n" style="color: #333;">sample_rate</span><span class="p">;</span></span>
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"></span>
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read the actual samples</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">rt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_samples</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hdf5_fil</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">channel_params</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">rt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_get_raw_samples</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">f5_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">read_nam</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">channel_params</span><span class="p">);</span></span>
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"></span>
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// trim using scrappie's internal method</span></span>
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314
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parameters taken directly from scrappie defaults</span></span>
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<li id="0cd5a7898ca2515cf6be03b2013fef5dda71d2cd">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#0cd5a7898ca2515cf6be03b2013fef5dda71d2cd"><strong>src/nanopolish_squiggle_read.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">@@ -15,6 +15,7 @@</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_eventalign.h"</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_read_db.h"</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_pore_model_set.h"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "nanopolish_fast5_io.h"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">PoreType</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">@@ -303,7 +304,7 @@ class SquiggleRead</td>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">load_from_events</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Load all read data from raw samples</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">load_from_raw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hid_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hd</span>f5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">load_from_raw</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fast5_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">f5_file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">);</span></span>
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307
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c"></span>
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308
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Version-specific intialization functions</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_load_R7</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">si</span><span class="p">);</span></span>
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<li id="8a4594db09bdbd5859ea2b82ef08bae7e6cb4eba">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#8a4594db09bdbd5859ea2b82ef08bae7e6cb4eba"><strong>src/nanopolish_vcf2fasta.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">@@ -47,6 +47,7 @@ static const char *VCF2FASTA_USAGE_MESSAGE =</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="s" style="color: #d14;">" --version display version</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="s" style="color: #d14;">" --help display this help and exit</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="s" style="color: #d14;">" -g, --genome=FILE the input genome is in FILE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="s" style="color: #d14;">" -f, --fofn=FILE read the list of VCF files to use from FILE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="s" style="color: #d14;">" --skip-checks skip the sanity checks</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Report bugs to "</span> <span class="n" style="color: #333;">PACKAGE_BUGREPORT</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,11 +55,12 @@ namespace opt</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">input_vcf_files</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">vcf_fofn</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">genome_file</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">skip_checks</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC61" 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;">shortopts</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"g:v"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC63" 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;">shortopts</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"g:<span class="idiff left right">f:</span>v"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span> <span class="n" style="color: #333;">OPT_HELP</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;">OPT_VERSION</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_SKIP_CHECKS</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC66" 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">@@ -67,7 +69,8 @@ static const struct option longopts[] = {</td>
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67
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_HELP</span> <span class="p">},</span></span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_VERSION</span> <span class="p">},</span></span>
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69
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"skip-checks"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_SKIP_CHECKS</span> <span class="p">},</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"genome"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"genome"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="p">{</span> <span class="s" style="color: #d14;">"fofn"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="sc" style="color: #d14;">'f'</span> <span class="p">},</span></span>
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71
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="p">{</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">}</span></span>
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72
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="p">};</span></span>
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73
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<td class="diff-line-num new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" 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="83" 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">@@ -80,6 +83,7 @@ void parse_vcf2fasta_options(int argc, char** argv)</td>
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80
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<td class="diff-line-num new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">:</span> <span class="n" style="color: #333;">die</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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81
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<td class="diff-line-num new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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82
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<td class="diff-line-num new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">genome_file</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vcf_fofn</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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83
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<td class="diff-line-num new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_SKIP_CHECKS</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">skip_checks</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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84
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_HELP</span><span class="p">:</span></span>
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85
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">VCF2FASTA_USAGE_MESSAGE</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" 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="99" 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">@@ -95,7 +99,7 @@ void parse_vcf2fasta_options(int argc, char** argv)</td>
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95
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">die</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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96
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="p">}</span></span>
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97
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">optind</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">optind</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vcf_fofn</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">SUBPROGRAM</span> <span class="s" style="color: #d14;">": not enough arguments</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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100
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">die</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="113" 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">@@ -109,6 +113,15 @@ void parse_vcf2fasta_options(int argc, char** argv)</td>
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109
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="n" style="color: #333;">optind</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">optind</span><span class="p">)</span> <span class="p">{</span></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">input_vcf_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">]);</span></span>
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111
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="p">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// add files from the fofn</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vcf_fofn</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">infile</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vcf_fofn</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</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;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">input_vcf_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">line</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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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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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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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">vcf2fasta_main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</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="n" style="color: #333;">argv</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -134,10 +147,10 @@ int vcf2fasta_main(int argc, char** argv)</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check for window coordinates</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">find</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"nanopolish_window"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">npos</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">'='</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">assert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">window_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fields</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">window_key</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"nanopolish_window="</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key_pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">find</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">window_key</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key_pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">npos</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">window_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">line</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">substr</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key_pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">window_key</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">())</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">v</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<li id="9186045b065422025ead086f2c07e4e27cd22c5e">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#9186045b065422025ead086f2c07e4e27cd22c5e"><strong>src/pore_model/nanopolish_builtin_models.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">@@ -21,6 +21,7 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_250bps_nucleotide_6mer_complement_pop2_model.inl"</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_250bps_nucleotide_6mer_template_model.inl"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_4_450bps_cpg_6mer_template_model.inl"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_4_450bps_gpc_6mer_template_model.inl"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_4_450bps_nucleotide_5mer_template_model.inl"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_4_450bps_nucleotide_6mer_template_model.inl"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "builtin_models/r9_4_70bps_u_to_t_rna_5mer_template_model.inl"</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">@@ -29,19 +30,20 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Autogenerated from convert_all_models.py</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PoreModel</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">builtin_models</span><span class="p">({</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_cpg_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_5mer_complement_pop1_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_5mer_complement_pop2_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_5mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_6mer_complement_pop1_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_6mer_complement_pop2_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_cpg_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_nucleotide_5mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_nucleotide_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_70bps_u_to_t_rna_5mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_dcm_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_dam_6mer_template_model_builtin</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_cpg_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_5mer_complement_pop1_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_5mer_complement_pop2_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_5mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_6mer_complement_pop1_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_6mer_complement_pop2_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_250bps_nucleotide_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_cpg_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_gpc_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_nucleotide_5mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_nucleotide_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_70bps_u_to_t_rna_5mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_dcm_6mer_template_model_builtin</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">initialize_r9_4_450bps_dam_6mer_template_model_builtin</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="p">});</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#40876473fea5fd59223a4e217ab3ce88ac23e944"><strong>src/thirdparty/scrappie/scrappie_common.c</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "scrappie_common.h"</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "scrappie_stdlib.h"</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//#include "util.h"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdbool.h></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">floatcmp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</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="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">-</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="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Quantiles from n array</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Using a relatively inefficent qsort resulting in O(n log n)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * performance but better performance is possible for small np.</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The array p is modified inplace, containing which quantiles to</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * calculation on input and the quantiles on output; on error, p</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * is filled with the value NAN.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to calculate quantiles from</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param nx Length of array x</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param p An array containing quantiles to calculate [in/out]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param np Length of array p</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return void</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">quantilef</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">np</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Sort array</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">space</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">space</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="p">}</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">space</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">space</span><span class="p">,</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">),</span> <span class="n" style="color: #333;">floatcmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Extract quantiles</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">nx</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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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">remf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">remf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">remf</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Should only occur when p is exactly 1.0</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">space</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Median of an array</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Using a relatively inefficent qsort resulting in O(n log n)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * performance but O(n) is possible.</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to calculate median of</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n Length of array</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return Median of array on success, NAN otherwise.</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">medianf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">quantilef</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</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="LC85" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Median Absolute Deviation of an array</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to calculate the MAD of</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n Length of array</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param med Median of the array. If NAN then median is calculated.</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return MAD of array on success, NAN otherwise.</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">madf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">med</span><span class="p">)</span> <span class="p">{</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mad_scaling_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4826</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="p">}</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="p">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">absdiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">absdiff</span><span class="p">)</span> <span class="p">{</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="p">}</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">_med</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">med</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">medianf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">med</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">absdiff</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabsf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_med</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">medianf</span><span class="p">(</span><span class="n" style="color: #333;">absdiff</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">absdiff</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad_scaling_factor</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"><span class="n" style="color: #333;">raw_table</span> <span class="nf" style="color: #900; font-weight: 600;">trim_and_segment_raw</span><span class="p">(</span><span class="n" style="color: #333;">raw_table</span> <span class="n" style="color: #333;">rt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim_start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim_end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">varseg_chunk</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">varseg_thresh</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">RETURN_NULL_IF</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">rt</span><span class="p">.</span><span class="n" style="color: #333;">raw</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">raw_table</span><span class="p">){</span><span class="mi" style="color: #099;">0</span><span class="p">});</span></span>
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<li id="eb73e696473ddc8d63df1f5a3399724c99cfa0da">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#eb73e696473ddc8d63df1f5a3399724c99cfa0da"><strong>src/thirdparty/scrappie/sse_mathfun.h</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* SIMD (SSE1+MMX or SSE2) implementation of sin, cos, exp and log</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Inspired by Intel Approximate Math library, and based on the</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> corresponding algorithms of the cephes math library</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> The default is to use the SSE1 version. If you define USE_SSE2 the</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> the SSE2 intrinsics will be used in place of the MMX intrinsics. Do</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> not expect any significant performance improvement with SSE2.</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Copyright (C) 2007 Julien Pommier</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This software is provided 'as-is', without any express or implied</span></span>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> warranty. In no event will the authors be held liable for any damages</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> arising from the use of this software.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Permission is granted to anyone to use this software for any purpose,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> including commercial applications, and to alter it and redistribute it</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> freely, subject to the following restrictions:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 1. The origin of this software must not be misrepresented; you must not</span></span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> claim that you wrote the original software. If you use this software</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> in a product, an acknowledgment in the product documentation would be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> appreciated but is not required.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 2. Altered source versions must be plainly marked as such, and must not be</span></span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> misrepresented as being the original software.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 3. This notice may not be removed or altered from any source distribution.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
29
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> (this is the zlib license)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
30
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Copyright (C) 2016 Oxford Nanopore technologies</span></span>
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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
34
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This software contain modifications (C) Oxford Nanopore Technologies</span></span>
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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
35
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> and is not the original software, which can be obtained from</span></span>
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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> http://gruntthepeon.free.fr/ssemath/</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma once</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef SSE_MATHFUN_H</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SSE_MATHFUN_H</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <xmmintrin.h></span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* yes I know, the top of this file is quite ugly */</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _MSC_VER </span><span class="cm" style="color: #998; font-style: italic;">/* visual c++ */</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define ALIGN16_BEG __declspec(align(16))</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define ALIGN16_END</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else </span><span class="cm" style="color: #998; font-style: italic;">/* gcc or icc */</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define ALIGN16_BEG</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define ALIGN16_END __attribute__((aligned(16)))</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* __m128 is ugly to write */</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">v4sf</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// vector of 4 float (sse1)</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <emmintrin.h></span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">v4si</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// vector of 4 int (sse2)</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">__m64</span> <span class="n" style="color: #333;">v2si</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// vector of 2 int (mmx)</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* declare some SSE constants -- why can't I figure a better way to do that? */</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _PS_CONST(Name, Val) \</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> static const ALIGN16_BEG float _ps_##Name[4] ALIGN16_END = { Val, Val, Val, Val }</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _PI32_CONST(Name, Val) \</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> static const ALIGN16_BEG int _pi32_##Name[4] ALIGN16_END = { Val, Val, Val, Val }</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _PS_CONST_TYPE(Name, Type, Val) \</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> static const ALIGN16_BEG Type _ps_##Name[4] ALIGN16_END = { Val, Val, Val, Val }</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">p5</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* the smallest non denormalized float number */</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST_TYPE</span><span class="p">(</span><span class="n" style="color: #333;">min_norm_pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="mh" style="color: #099;">0x00800000</span><span class="p">);</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST_TYPE</span><span class="p">(</span><span class="n" style="color: #333;">mant_mask</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="mh" style="color: #099;">0x7f800000</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST_TYPE</span><span class="p">(</span><span class="n" style="color: #333;">inv_mant_mask</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="o" style="font-weight: 600;">~</span><span class="mh" style="color: #099;">0x7f800000</span><span class="p">);</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST_TYPE</span><span class="p">(</span><span class="n" style="color: #333;">sign_mask</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="mh" style="color: #099;">0x80000000</span><span class="p">);</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST_TYPE</span><span class="p">(</span><span class="n" style="color: #333;">inv_sign_mask</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="o" style="font-weight: 600;">~</span><span class="mh" style="color: #099;">0x80000000</span><span class="p">);</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="n" style="color: #333;">_PI32_CONST</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="c"><span class="n" style="color: #333;">_PI32_CONST</span><span class="p">(</span><span class="n" style="color: #333;">inv1</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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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="n" style="color: #333;">_PI32_CONST</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"><span class="n" style="color: #333;">_PI32_CONST</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"><span class="n" style="color: #333;">_PI32_CONST</span><span class="p">(</span><span class="mh" style="color: #099;">0x7f</span><span class="p">,</span> <span class="mh" style="color: #099;">0x7f</span><span class="p">);</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_SQRTHF</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">707106781186547524</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
90
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p0</span><span class="p">,</span> <span class="mf" style="color: #099;">7.0376836292E-2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.1514610310E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.1676998740E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.2420140846E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1.4249322787E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1.6668057665E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">2.0000714765E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p7</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">2.4999993993E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_p8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">3.3333331174E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
99
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_q1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">2.12194440e-4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_log_q2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">693359375</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_SSE2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">union</span> <span class="n" style="color: #333;">xmm_mm_union</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">xmm</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">__m64</span> <span class="n" style="color: #333;">mm</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">xmm_mm_union</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define COPY_XMM_TO_MM(xmm_, mm0_, mm1_) { \</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> xmm_mm_union u; u.xmm = xmm_; \</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> mm0_ = u.mm[0]; \</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> mm1_ = u.mm[1]; \</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define COPY_MM_TO_XMM(mm0_, mm1_, xmm_) { \</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> xmm_mm_union u; u.mm[0]=mm0_; u.mm[1]=mm1_; xmm_ = u.xmm; \</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif // USE_SSE2</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* natural logarithm computed for 4 simultaneous float</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> return NaN for x <= 0</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">v4sf</span> <span class="nf" style="color: #900; font-weight: 600;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">log_ps</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">v4si</span> <span class="n" style="color: #333;">emm0</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">v2si</span> <span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">;</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_1</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">invalid_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmple_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">());</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_min_norm_pos</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* cut off denormalized stuff */</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_SSE2</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* part 1: x = frexpf(x, &e); */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">COPY_XMM_TO_MM</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_srli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_srli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_srli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castps_si128</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="mi" style="color: #099;">23</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* keep only the fractional part */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_inv_mant_mask</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_or_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_0p5</span><span class="p">);</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_SSE2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* now e=mm0:mm1 contain the really base-2 exponent */</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_0x7f</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_0x7f</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtpi32x2_ps</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">);</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">_mm_empty</span><span class="p">();</span> <span class="cm" style="color: #998; font-style: italic;">/* bye bye mmx */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_0x7f</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtepi32_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">);</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* part2:</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if( x < SQRTHF ) {</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> e -= 1;</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x = x + x - 1.0;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> } else { x = x - 1.0; }</span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmplt_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_SQRTHF</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">one</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">));</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p2</span><span class="p">);</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
187
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p6</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p7</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
191
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_p8</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
192
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
194
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_q1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
198
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="c"></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_0p5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
202
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
204
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_log_q2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
205
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
206
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_or_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">invalid_mask</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// negative arg will be NAN</span></span>
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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
208
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"><span class="p">}</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">exp_hi</span><span class="p">,</span> <span class="mi" style="color: #099;">88</span><span class="p">.</span><span class="mi" style="color: #099;">3762626647949</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">exp_lo</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">88</span><span class="p">.</span><span class="mi" style="color: #099;">3762626647949</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c"></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_LOG2EF</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">44269504088896341</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_C1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">693359375</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_C2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">2.12194440e-4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_p0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.9875691500E-4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_p1</span><span class="p">,</span> <span class="mf" style="color: #099;">1.3981999507E-3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_p2</span><span class="p">,</span> <span class="mf" style="color: #099;">8.3334519073E-3</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_p3</span><span class="p">,</span> <span class="mf" style="color: #099;">4.1665795894E-2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_p4</span><span class="p">,</span> <span class="mf" style="color: #099;">1.6666665459E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_exp_p5</span><span class="p">,</span> <span class="mf" style="color: #099;">5.0000001201E-1</span><span class="p">);</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c"></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="nf" style="color: #900; font-weight: 600;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">exp_ps</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">(),</span> <span class="n" style="color: #333;">fx</span><span class="p">;</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">v4si</span> <span class="n" style="color: #333;">emm0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">v2si</span> <span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_min_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_exp_hi</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_exp_lo</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* express exp(x) as exp(g + n*log(2)) */</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">fx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_LOG2EF</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"> <span class="n" style="color: #333;">fx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_0p5</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* how to perform a floorf with SSE: just below */</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_SSE2</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* step 1 : cast to int */</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movehl_ps</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* step 2 : cast back to float */</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtpi32x2_ps</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">);</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_epi32</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtepi32_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">);</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* if greater, substract 1 */</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_ps</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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255
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">fx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">);</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_C1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_C2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_p0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_p1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
269
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_p2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
270
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_p3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_p4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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275
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_exp_p5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* build 2^n */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_SSE2</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movehl_ps</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_0x7f</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_0x7f</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">pow2n</span><span class="p">;</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">pow2n</span><span class="p">);</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"> <span class="n" style="color: #333;">_mm_empty</span><span class="p">();</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_epi32</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">);</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_0x7f</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="mi" style="color: #099;">23</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">pow2n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">);</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">pow2n</span><span class="p">);</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"><span class="p">}</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">minus_cephes_DP1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">78515625</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">minus_cephes_DP2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">2.4187564849853515625e-4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">minus_cephes_DP3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">3.77489497744594108e-8</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">sincof_p0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.9515295891E-4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">sincof_p1</span><span class="p">,</span> <span class="mf" style="color: #099;">8.3321608736E-3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">sincof_p2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.6666654611E-1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">coscof_p0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.443315711809948E-005</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">coscof_p1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.388731625493765E-003</span><span class="p">);</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">coscof_p2</span><span class="p">,</span> <span class="mf" style="color: #099;">4.166664568298827E-002</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="c"><span class="n" style="color: #333;">_PS_CONST</span><span class="p">(</span><span class="n" style="color: #333;">cephes_FOPI</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">27323954473516</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// 4 / M_PI</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* evaluation of 4 sines at onces, using only SSE1+MMX intrinsics so</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it runs also on old athlons XPs and the pentium III of your grand</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> mother.</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> The code is the exact rewriting of the cephes sinf function.</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Precision is excellent as long as x < 8192 (I did not bother to</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> take into account the special handling they have for greater values</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> -- it does not return garbage for arguments over 8192, though, but</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> the extra precision is missing).</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Note that it is such that sinf((float)M_PI) = 8.74e-8, which is the</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> surprising but correct result.</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Performance is also surprisingly good, 1.33 times faster than the</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> macos vsinf SSE2 function, and 1.5 times faster than the</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> __vrs4_sinf of amd's ACML (which is only available in 64 bits). Not</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> too bad for an SSE1 function (with no special tuning) !</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> However the latter libraries probably have a much better handling of NaN,</span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Inf, denormalized and other special arguments..</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> On my core 1 duo, the execution of this function takes approximately 95 cycles.</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> From what I have observed on the experiments with Intel AMath lib, switching to an</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> SSE2 version would improve the perf by only 10%.</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Since it is based on SSE intrinsics, it has to be compiled at -O2 to</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> deliver full speed.</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">v4sf</span> <span class="nf" style="color: #900; font-weight: 600;">sin_ps</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// any x</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">xmm1</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">(),</span> <span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">v4si</span> <span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="n" style="color: #333;">emm2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">v2si</span> <span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* take the absolute value */</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_inv_sign_mask</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* extract the sign bit (upper one) */</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">sign_bit</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sign_mask</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* scale by 4/Pi */</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_FOPI</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store the integer part of y in mm0 */</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_epi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j=(j+1) & (~1) (see the cephes sources) */</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtepi32_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the swap sign flag */</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the polynom selection mask</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> there is one polynom for 0 <= x <= Pi/4</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> and another one for Pi/4<x<=Pi/2</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Both branches will be computed.</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si128</span><span class="p">());</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="c"></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">swap_sign_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">);</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">poly_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">);</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">sign_bit</span><span class="p">,</span> <span class="n" style="color: #333;">swap_sign_bit</span><span class="p">);</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="c"></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store the integer part of y in mm0:mm1 */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movehl_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j=(j+1) & (~1) (see the cephes sources) */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtpi32x2_ps</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the swap sign flag */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the polynom selection mask */</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si64</span><span class="p">());</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si64</span><span class="p">());</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">swap_sign_bit</span><span class="p">,</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">;</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">swap_sign_bit</span><span class="p">);</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">);</span></span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">sign_bit</span><span class="p">,</span> <span class="n" style="color: #333;">swap_sign_bit</span><span class="p">);</span></span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">_mm_empty</span><span class="p">();</span> <span class="cm" style="color: #998; font-style: italic;">/* good-bye mmx */</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* The magic pass: "Extended precision modular arithmetic"</span></span>
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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x = ((x - y * DP1) - y * DP2) - y * DP3; */</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP1</span><span class="p">;</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP2</span><span class="p">;</span></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP3</span><span class="p">;</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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418
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"></span>
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424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Evaluate the first polynom (0 <= x <= Pi/4) */</span></span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p0</span><span class="p">;</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="c"></span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p1</span><span class="p">);</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p2</span><span class="p">);</span></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_0p5</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_1</span><span class="p">);</span></span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Evaluate the second polynom (Pi/4 <= x <= 0) */</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p0</span><span class="p">;</span></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p1</span><span class="p">);</span></span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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444
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p2</span><span class="p">);</span></span>
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445
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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446
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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447
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* select the correct result from the two polynoms */</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">;</span></span>
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451
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//, xmm3);</span></span>
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452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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453
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span><span class="n" style="color: #333;">y2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update the sign */</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* almost the same as sin_ps */</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">v4sf</span> <span class="nf" style="color: #900; font-weight: 600;">cos_ps</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// any x</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">xmm1</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">(),</span> <span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="c"> <span class="n" style="color: #333;">v4si</span> <span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="n" style="color: #333;">emm2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="c"> <span class="n" style="color: #333;">v2si</span> <span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* take the absolute value */</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_inv_sign_mask</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* scale by 4/Pi */</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_FOPI</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store the integer part of y in mm0 */</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_epi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j=(j+1) & (~1) (see the cephes sources) */</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtepi32_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the swap sign flag */</span></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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486
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the polynom selection mask */</span></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si128</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">sign_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">poly_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store the integer part of y in mm0:mm1 */</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movehl_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="c"></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j=(j+1) & (~1) (see the cephes sources) */</span></span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="c"></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtpi32x2_ps</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">);</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="c"></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="c"></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the swap sign flag in mm0:mm1 and the</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> polynom selection mask in mm2:mm3 */</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="c"></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="c"></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si64</span><span class="p">());</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si64</span><span class="p">());</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="c"></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">sign_bit</span><span class="p">,</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">;</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit</span><span class="p">);</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">);</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;">_mm_empty</span><span class="p">();</span> <span class="cm" style="color: #998; font-style: italic;">/* good-bye mmx */</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* The magic pass: "Extended precision modular arithmetic"</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x = ((x - y * DP1) - y * DP2) - y * DP3; */</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP1</span><span class="p">;</span></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP2</span><span class="p">;</span></span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP3</span><span class="p">;</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Evaluate the first polynom (0 <= x <= Pi/4) */</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_0p5</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Evaluate the second polynom (Pi/4 <= x <= 0) */</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p0</span><span class="p">;</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p1</span><span class="p">);</span></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p2</span><span class="p">);</span></span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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563
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="c"></span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* select the correct result from the two polynoms */</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">;</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//, xmm3);</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span><span class="n" style="color: #333;">y2</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update the sign */</span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit</span><span class="p">);</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="c"></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="c"><span class="p">}</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="c"></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* since sin_ps and cos_ps are almost identical, sincos_ps could replace both of them..</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> it is almost as fast, and gives you a free cosine with your sine */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">sincos_ps</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v4sf</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">v4sf</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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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">xmm1</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">(),</span> <span class="n" style="color: #333;">sign_bit_sin</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="c"> <span class="n" style="color: #333;">v4si</span> <span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="n" style="color: #333;">emm4</span><span class="p">;</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;">v2si</span> <span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">mm4</span><span class="p">,</span> <span class="n" style="color: #333;">mm5</span><span class="p">;</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit_sin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* take the absolute value */</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_inv_sign_mask</span><span class="p">);</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* extract the sign bit (upper one) */</span></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit_sin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">sign_bit_sin</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sign_mask</span><span class="p">);</span></span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="c"></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* scale by 4/Pi */</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_cephes_FOPI</span><span class="p">);</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="c"></span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store the integer part of y in emm2 */</span></span>
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597
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_epi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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598
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="c"></span>
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599
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j=(j+1) & (~1) (see the cephes sources) */</span></span>
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600
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
601
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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602
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtepi32_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="c"></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="c"> <span class="n" style="color: #333;">emm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">emm2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="c"></span>
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606
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the swap sign flag for the sine */</span></span>
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607
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="c"> <span class="n" style="color: #333;">emm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">swap_sign_bit_sin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm0</span><span class="p">);</span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="c"></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the polynom selection mask for the sine*/</span></span>
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612
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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613
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="c"> <span class="n" style="color: #333;">emm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si128</span><span class="p">());</span></span>
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614
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">poly_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm2</span><span class="p">);</span></span>
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615
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* store the integer part of y in mm2:mm3 */</span></span>
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617
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movehl_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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619
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvttps_pi32</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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620
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="c"></span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* j=(j+1) & (~1) (see the cephes sources) */</span></span>
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622
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_1</span><span class="p">);</span></span>
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624
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_inv1</span><span class="p">);</span></span>
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626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="c"></span>
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627
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtpi32x2_ps</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">);</span></span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="c"></span>
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629
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="c"> <span class="n" style="color: #333;">mm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mm2</span><span class="p">;</span></span>
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630
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="c"> <span class="n" style="color: #333;">mm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mm3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the swap sign flag for the sine */</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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635
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">mm0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="c"> <span class="n" style="color: #333;">mm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">swap_sign_bit_sin</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm0</span><span class="p">,</span> <span class="n" style="color: #333;">mm1</span><span class="p">,</span> <span class="n" style="color: #333;">swap_sign_bit_sin</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the polynom selection mask for the sine */</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="c"> <span class="n" style="color: #333;">mm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si64</span><span class="p">());</span></span>
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645
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="c"> <span class="n" style="color: #333;">mm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_si64</span><span class="p">());</span></span>
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646
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">;</span></span>
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647
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm2</span><span class="p">,</span> <span class="n" style="color: #333;">mm3</span><span class="p">,</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">);</span></span>
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648
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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649
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="c"></span>
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650
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* The magic pass: "Extended precision modular arithmetic"</span></span>
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651
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> x = ((x - y * DP1) - y * DP2) - y * DP3; */</span></span>
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652
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP1</span><span class="p">;</span></span>
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653
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP2</span><span class="p">;</span></span>
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654
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_minus_cephes_DP3</span><span class="p">;</span></span>
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655
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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656
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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658
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm1</span><span class="p">);</span></span>
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659
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm2</span><span class="p">);</span></span>
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660
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">xmm3</span><span class="p">);</span></span>
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661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="c"></span>
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662
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_SSE2</span></span>
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663
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="c"> <span class="n" style="color: #333;">emm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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664
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="c"> <span class="n" style="color: #333;">emm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_si128</span><span class="p">(</span><span class="n" style="color: #333;">emm4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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665
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="c"> <span class="n" style="color: #333;">emm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_epi32</span><span class="p">(</span><span class="n" style="color: #333;">emm4</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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666
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">sign_bit_cos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">emm4</span><span class="p">);</span></span>
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667
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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668
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get the sign flag for the cosine */</span></span>
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669
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="c"> <span class="n" style="color: #333;">mm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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670
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="c"> <span class="n" style="color: #333;">mm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_2</span><span class="p">);</span></span>
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671
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="c"> <span class="n" style="color: #333;">mm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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672
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="c"> <span class="n" style="color: #333;">mm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_si64</span><span class="p">(</span><span class="n" style="color: #333;">mm5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v2si</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_pi32_4</span><span class="p">);</span></span>
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673
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="c"> <span class="n" style="color: #333;">mm4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm4</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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674
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="c"> <span class="n" style="color: #333;">mm5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_pi32</span><span class="p">(</span><span class="n" style="color: #333;">mm5</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">);</span></span>
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675
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">sign_bit_cos</span><span class="p">;</span></span>
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676
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="c"> <span class="n" style="color: #333;">COPY_MM_TO_XMM</span><span class="p">(</span><span class="n" style="color: #333;">mm4</span><span class="p">,</span> <span class="n" style="color: #333;">mm5</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit_cos</span><span class="p">);</span></span>
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677
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="c"> <span class="n" style="color: #333;">_mm_empty</span><span class="p">();</span> <span class="cm" style="color: #998; font-style: italic;">/* good-bye mmx */</span></span>
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678
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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679
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="c"></span>
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680
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="c"> <span class="n" style="color: #333;">sign_bit_sin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">sign_bit_sin</span><span class="p">,</span> <span class="n" style="color: #333;">swap_sign_bit_sin</span><span class="p">);</span></span>
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681
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="c"></span>
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682
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="c"></span>
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683
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Evaluate the first polynom (0 <= x <= Pi/4) */</span></span>
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684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="c"></span>
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687
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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688
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p1</span><span class="p">);</span></span>
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689
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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690
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_coscof_p2</span><span class="p">);</span></span>
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691
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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692
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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693
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_0p5</span><span class="p">);</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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695
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_1</span><span class="p">);</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="c"></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Evaluate the second polynom (Pi/4 <= x <= 0) */</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="c"></span>
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p0</span><span class="p">;</span></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p1</span><span class="p">);</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v4sf</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_ps_sincof_p2</span><span class="p">);</span></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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705
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_mul_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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706
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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707
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="c"></span>
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708
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* select the correct result from the two polynoms */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
709
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="c"> <span class="n" style="color: #333;">xmm3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">poly_mask</span><span class="p">;</span></span>
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710
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">ysin2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y2</span><span class="p">);</span></span>
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711
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="c"> <span class="n" style="color: #333;">v4sf</span> <span class="n" style="color: #333;">ysin1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_andnot_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm3</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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712
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="c"> <span class="n" style="color: #333;">y2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">y2</span><span class="p">,</span><span class="n" style="color: #333;">ysin2</span><span class="p">);</span></span>
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713
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="c"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">ysin1</span><span class="p">);</span></span>
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714
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="c"></span>
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715
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="c"> <span class="n" style="color: #333;">xmm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">ysin1</span><span class="p">,</span><span class="n" style="color: #333;">ysin2</span><span class="p">);</span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="c"> <span class="n" style="color: #333;">xmm2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span><span class="n" style="color: #333;">y2</span><span class="p">);</span></span>
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717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="c"></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update the sign */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
719
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm1</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit_sin</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
720
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_xor_ps</span><span class="p">(</span><span class="n" style="color: #333;">xmm2</span><span class="p">,</span> <span class="n" style="color: #333;">sign_bit_cos</span><span class="p">);</span></span>
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721
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="c"><span class="p">}</span></span>
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722
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/* SSE_MATHFUN_H */</span></span></pre>
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<li id="1b1d273af27cf998f7a24ba41cfa22a7da674993">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#1b1d273af27cf998f7a24ba41cfa22a7da674993"><strong>src/thirdparty/scrappie/util.c</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Too many calls to quantile lead to high failure rate for `scrappie raw`</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define BANANA 1</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <err.h></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "scrappie_stdlib.h"</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">argmaxf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">n</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="LC11" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">imax</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="LC15" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">vmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vmax</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"> <span class="n" style="color: #333;">vmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"> <span class="n" style="color: #333;">imax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">imax</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">argminf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">n</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="LC27" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">imin</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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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">vmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vmin</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">vmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">imin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">imin</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">valmaxf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">n</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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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">vmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vmax</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">vmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vmax</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">valminf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">n</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="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">vmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vmin</span><span class="p">)</span> <span class="p">{</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">vmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vmin</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">floatcmp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</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="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">-</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="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Quantiles from n array</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Using a relatively inefficent qsort resulting in O(n log n)</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * performance but better performance is possible for small np.</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The array p is modified inplace, containing which quantiles to</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * calculation on input and the quantiles on output; on error, p</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * is filled with the value NAN.</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to calculate quantiles from</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param nx Length of array x</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param p An array containing quantiles to calculate [in/out]</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param np Length of array p</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return void</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">quantilef</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">np</span><span class="p">)</span> <span class="p">{</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"> <span class="p">}</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"> <span class="p">}</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> <span class="p">}</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="p">}</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Sort array</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">space</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">space</span><span class="p">)</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="p">}</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"> <span class="p">}</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">space</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">space</span><span class="p">,</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">),</span> <span class="n" style="color: #333;">floatcmp</span><span class="p">);</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Extract quantiles</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">np</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">nx</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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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">remf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">remf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">remf</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">idx</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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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Should only occur when p is exactly 1.0</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">space</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">];</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="p">}</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"> <span class="p">}</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">space</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Median of an array</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Using a relatively inefficent qsort resulting in O(n log n)</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * performance but O(n) is possible.</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to calculate median of</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n Length of array</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return Median of array on success, NAN otherwise.</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">medianf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">quantilef</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Median Absolute Deviation of an array</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to calculate the MAD of</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n Length of array</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param med Median of the array. If NAN then median is calculated.</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return MAD of array on success, NAN otherwise.</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">madf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">med</span><span class="p">)</span> <span class="p">{</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mad_scaling_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">4826</span><span class="p">;</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">absdiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">absdiff</span><span class="p">)</span> <span class="p">{</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NAN</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="p">}</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">_med</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">med</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">medianf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">med</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">absdiff</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabsf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_med</span><span class="p">);</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"> <span class="p">}</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">medianf</span><span class="p">(</span><span class="n" style="color: #333;">absdiff</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">absdiff</span><span class="p">);</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad_scaling_factor</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"><span class="p">}</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Med-MAD normalisation of an array</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Normalise an array using the median and MAD as measures of</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * location and scale respectively. The array is updated inplace.</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array containing values to normalise</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n Length of array</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return void</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">medmad_normalise_array</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="c"> <span class="p">}</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="p">}</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="c"></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">xmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">medianf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">xmad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">madf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">xmed</span><span class="p">);</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">xmed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">xmad</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="p">}</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="c"></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** Studentise array using Kahan summation algorithm</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Studentise an array using the Kahan summation</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * algorithm for numerical stability. The array is updated inplace.</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * https://en.wikipedia.org/wiki/Kahan_summation_algorithm</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param x An array to normalise</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n Length of array</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return void</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">studentise_array_kahan</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">sumsq</span><span class="p">,</span> <span class="n" style="color: #333;">comp</span><span class="p">,</span> <span class="n" style="color: #333;">compsq</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"> <span class="n" style="color: #333;">sumsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">comp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">comp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">comp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sum_tmp</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d1</span><span class="p">;</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum_tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">compsq</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumsq_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumsq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">compsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sumsq_tmp</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sumsq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">d2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">sumsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumsq_tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">sumsq</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">sumsq</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sum</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">sumsq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">sumsq</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">sumf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sum</span><span class="p">;</span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">sumsqf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumsq</span><span class="p">;</span></span>
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242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sumf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sumsqf</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">equality_array</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tol</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">){</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tol</span><span class="p">){</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"Failure at elt %zu: %f %f</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="p">}</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"><span class="p">}</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">equality_arrayf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tol</span><span class="p">){</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">){</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="c"> <span class="p">}</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fabsf</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tol</span><span class="p">){</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c"> <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"Failure at elt %zu: %f %f</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"> <span class="p">}</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"><span class="p">}</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">equality_arrayi</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">){</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"> <span class="p">}</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="n" style="color: #333;">warnx</span><span class="p">(</span><span class="s" style="color: #d14;">"Failure at elt %zu: %d %d</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> <span class="p">}</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="p">}</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"><span class="p">}</span></span></pre>
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<li id="6460fdb9758236251f67bb5fb70fe7eea56b0114">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#6460fdb9758236251f67bb5fb70fe7eea56b0114"><strong>src/thirdparty/scrappie/util.h</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma once</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef UTIL_H</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define UTIL_H</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <immintrin.h></span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <math.h></span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <stdbool.h></span></span>
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7
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <stdint.h></span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include <stdio.h></span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># include "sse_mathfun.h"</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef FAST_LOG</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define LOGFV fast_logfv</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define LOGFV logfv</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef FAST_EXP</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define EXPFV fast_expfv</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define EXPFV expfv</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef FAST_TANH</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define TANHFV fast_tanhfv</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define TANHFV tanhfv</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef FAST_LOGISTIC</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define LOGISTICFV fast_logisticfv</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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32
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define LOGISTICFV logisticfv</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># ifdef FAST_ELU</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define ELUFV fast_elufv</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define ELUFV elufv</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Create a vector of ones. */</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kr" style="font-weight: 600;">__inline</span> <span class="n" style="color: #333;">__m128</span> <span class="nf" style="color: #900; font-weight: 600;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__gnu_inline__</span><span class="p">,</span> <span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">__extension__</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kr" style="font-weight: 600;">__inline</span> <span class="n" style="color: #333;">__m128d</span> <span class="nf" style="color: #900; font-weight: 600;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__gnu_inline__</span><span class="p">,</span> <span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">_mm_setone_pd</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">__extension__</span><span class="p">(</span><span class="n" style="color: #333;">__m128d</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Standard implementations</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">logisticf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">expf</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">eluf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">){</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">expm1f</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Constants for fast exp approximation. See Schraudolph (1999)</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define _A 12102203.161561485f</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Minimum maximum relative error</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//# define _B 1064986822.5027076f</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// No bias at zero</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define _B 1065353216.0f</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Minimum RMS relative error</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//# define _B 1064866803.6193156f</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Minimum mean relative error</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//# define _B 1064807268.0425934f</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define _BOUND 88.02969193111305</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fast_expf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fmaxf</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">_BOUND</span><span class="p">,</span> <span class="n" style="color: #333;">fminf</span><span class="p">(</span><span class="n" style="color: #333;">_BOUND</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="k" style="font-weight: 600;">union</span> <span class="p">{</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"> <span class="p">}</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="p">.</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</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;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_B</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="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"><span class="p">}</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fast_logisticf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fast_expf</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="p">}</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fast_tanhf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast_logisticf</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"><span class="p">}</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fast_eluf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">){</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">fast_expf</span><span class="p">(</span><span class="n" style="color: #333;">x</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 class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"><span class="p">}</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Vectorised functions</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">expfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">__v4sf</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="n" style="color: #333;">exp_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"><span class="p">}</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">logfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">__v4sf</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
110
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="n" style="color: #333;">log_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"><span class="p">}</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">logisticfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">ones</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_div_ps</span><span class="p">(</span><span class="n" style="color: #333;">ones</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">ones</span><span class="p">,</span> <span class="n" style="color: #333;">expfv</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">x</span><span class="p">)));</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"><span class="p">}</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">tanhfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logisticfv</span><span class="p">(</span><span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">),</span> <span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">());</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"><span class="p">}</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">elufv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)){</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// All positive, early return.</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"> <span class="p">}</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpge_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">());</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expfv</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">();</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_or_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">_mm_andnot_ps</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">));</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"><span class="p">}</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Fast vectorised approximations</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">fast_expfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">_A</span><span class="p">,</span> <span class="n" style="color: #333;">_A</span><span class="p">,</span> <span class="n" style="color: #333;">_A</span><span class="p">,</span> <span class="n" style="color: #333;">_A</span> <span class="p">};</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">_B</span><span class="p">,</span> <span class="n" style="color: #333;">_B</span><span class="p">,</span> <span class="n" style="color: #333;">_B</span><span class="p">,</span> <span class="n" style="color: #333;">_B</span> <span class="p">};</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">_BOUND</span><span class="p">,</span> <span class="n" style="color: #333;">_BOUND</span><span class="p">,</span> <span class="n" style="color: #333;">_BOUND</span><span class="p">,</span> <span class="n" style="color: #333;">_BOUND</span> <span class="p">};</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_ps</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">_bound</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_min_ps</span><span class="p">(</span><span class="n" style="color: #333;">_bound</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_cvtps_epi32</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">fast_logfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define _Alogfv 8.262958294867817e-08f</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># define _Blogfv 1064872507.1541044f</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">_Alogfv</span><span class="p">,</span> <span class="n" style="color: #333;">_Alogfv</span><span class="p">,</span> <span class="n" style="color: #333;">_Alogfv</span><span class="p">,</span> <span class="n" style="color: #333;">_Alogfv</span> <span class="p">};</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">__v4sf</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">_Blogfv</span><span class="p">,</span> <span class="n" style="color: #333;">_Blogfv</span><span class="p">,</span> <span class="n" style="color: #333;">_Blogfv</span><span class="p">,</span> <span class="n" style="color: #333;">_Blogfv</span> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cvtepi32_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castps_si128</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"><span class="p">}</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">fast_logisticfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_rcp_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">(),</span> <span class="n" style="color: #333;">fast_expfv</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">x</span><span class="p">)));</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"><span class="p">}</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">fast_tanhfv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast_logisticfv</span><span class="p">(</span><span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">));</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_sub_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_add_ps</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">),</span> <span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">());</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"><span class="p">}</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">__attribute__</span> <span class="p">((</span><span class="n" style="color: #333;">__always_inline__</span><span class="p">))</span> <span class="n" style="color: #333;">fast_elufv</span><span class="p">(</span><span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)){</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// All positive, early return.</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="p">}</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpge_ps</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_setzero_ps</span><span class="p">());</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast_expfv</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_mm_setone_ps</span><span class="p">();</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_or_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_and_ps</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">_mm_andnot_ps</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">));</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="c"></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argmaxf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argminf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">valmaxf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">valminf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">iceil</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">ifloor</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="p">{</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"><span class="p">}</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">quantilef</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">np</span><span class="p">);</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">medianf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">madf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">med</span><span class="p">);</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">medmad_normalise_array</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">studentise_array_kahan</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">equality_array</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tol</span><span class="p">);</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">equality_arrayf</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">tol</span><span class="p">);</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">equality_arrayi</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/* UTIL_H */</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/64e79bf282fc4c2aaad5fe45bfac8226b79d97bd#4547105bf53f4c152441673b657f1f5a56f0b6fd"><strong>src/training_core.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">@@ -8,18 +8,12 @@ using std::vector;</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">multiset</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</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="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">use_multiset_logsum</span> <span class="o" style="font-weight: 600;">=</span> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_MULTISET_LOGSUM</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">use_multiset_logsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="n" style="color: #333;">ParamMixture</span> <span class="nf" style="color: #900; font-weight: 600;">train_gaussian_mixture</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">StateTrainingData</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ParamMixture</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">input_mixture</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_components</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_mixture</span><span class="p">.</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">log_n_data</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;">log</span><span class="p">(</span><span class="n" style="color: #333;">n_data</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">input_mixture</span><span class="p">.</span><span class="n" style="color: #333;">log_weights</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="n" style="color: #333;">n_components</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">ParamMixture</span> <span class="n" style="color: #333;">curr_mixture</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_mixture</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" 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">@@ -76,6 +70,16 @@ ParamMixture train_gaussian_mixture(const vector< StateTrainingData >& data, con</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// compute logsum</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">logsumset</span><span class="o" style="font-weight: 600;"><</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">denom_terms</span><span class="p">(</span><span class="n" style="color: #333;">use_multiset_logsum</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" 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;">size_t</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_components</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" 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;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_data</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">denom_terms</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">log_resp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="p">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">log_n_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">denom_terms</span><span class="p">.</span><span class="n" style="color: #333;">val</span><span class="p">();</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"></span>
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79
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// update weights</span></span>
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80
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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81
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// w'[j] := sum_i resp[i][j] / n_data</span></span>
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