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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pybigwig">Debian Med / pybigwig</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e">a6dedc88</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T16:32:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.18+dfsg</pre>
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</ul>
<h4>9 changed files:</h4>
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<a href="#1de6ece0cbc2ded411141df6da5b9efc91345fbb">
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+
.environmentLinux.yaml
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<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
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+
.github/workflows/build.yml
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<li class="file-stats">
<a href="#754d5aad863c8a48ee5a23e6f583957700a28b7c">
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+
.github/workflows/pypi.yml
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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−
.travis.yml
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#ae58b3ba4c54b6fadb279decb1690b71b8be4857">
pyBigWig.c
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<li class="file-stats">
<a href="#a53acb6d60ac6a063886d0a7a1dd8f7184e6f980">
pyBigWig.h
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<li class="file-stats">
<a href="#f5d848e7beeea87ec3202f19ebf1bce809c843bd">
pyBigWigTest/test.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="1de6ece0cbc2ded411141df6da5b9efc91345fbb">
<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#1de6ece0cbc2ded411141df6da5b9efc91345fbb"><strong>.environmentLinux.yaml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">foo</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">channels</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda-forge</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bioconda</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">default</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">dependencies</span><span class="pi">:</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc_linux-64</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">curl</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;">zlib</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python </span><span class="m" style="color: #099;">3.8</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">numpy</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nose</span></span></pre>
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<li id="fe77d5d1439f26e353a42bbd38dece2467ff6558">
<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#fe77d5d1439f26e353a42bbd38dece2467ff6558"><strong>.github/workflows/build.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> <span class="s" style="color: #d14;">pull_request</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">testLinux</span><span class="pi">:</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">TestLinux</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">ubuntu-latest"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">defaults</span><span class="pi">:</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">shell</span><span class="pi">:</span> <span class="s" style="color: #d14;">bash -l {0}</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">conda-incubator/setup-miniconda@v2</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">activate-environment</span><span class="pi">:</span> <span class="s" style="color: #d14;">foo</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">environment-file</span><span class="pi">:</span> <span class="s" style="color: #d14;">.environmentLinux.yaml</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">auto-activate-base</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</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="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="s" style="color: #d14;">pip install .</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="s" style="color: #d14;">nosetests -sv</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#754d5aad863c8a48ee5a23e6f583957700a28b7c"><strong>.github/workflows/pypi.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">push</span><span class="pi">]</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">pypi</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">upload to pypi</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v1</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="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup conda</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="s" style="color: #d14;">curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="s" style="color: #d14;">bash miniconda.sh -b -p $HOME/miniconda</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="s" style="color: #d14;">export PATH="$HOME/miniconda/bin:$PATH"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="s" style="color: #d14;">hash -r</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="s" style="color: #d14;">conda config --set always_yes yes --set changeps1 no</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">create env</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="s" style="color: #d14;">export PATH=$HOME/miniconda/bin:$PATH</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="s" style="color: #d14;">conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 twine numpy libcurl curl zlib</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">sdist</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="s" style="color: #d14;">export PATH=$HOME/miniconda/bin:$PATH</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="s" style="color: #d14;">source activate foo</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">rm -f dist/*</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">python setup.py sdist</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">upload</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">TWINE_USERNAME</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">__token__"</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">TWINE_PASSWORD</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.pypi_password }}</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="s" style="color: #d14;">export PATH=$HOME/miniconda/bin:$PATH</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="s" style="color: #d14;">source activate foo</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="s" style="color: #d14;">twine upload dist/*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install numpy && python ./setup.py install</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</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="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">nosetests -sv</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,6 +7,7 @@ Table of Contents</td>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=================</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Requirements</span><span class="p">](</span><span class="sx" style="color: #d14;">#requirements</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage</span><span class="p">)</span></span>
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11
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Load the extension</span><span class="p">](</span><span class="sx" style="color: #d14;">#load-the-extension</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Open a bigWig or bigBed file</span><span class="p">](</span><span class="sx" style="color: #d14;">#open-a-bigwig-or-bigbed-file</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" 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">@@ -34,9 +35,16 @@ You can install this extension directly from github with:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown">or with conda</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install pybigwig -c bioconda</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install pybigwig -c <span class="idiff left right">conda-forge -c </span>bioconda</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">Note that libcurl (and the <span class="sb" style="color: #d14;">`curl-config`</span> command) are required for installation. This is typically already installed on many Linux and OSX systems (if you install with conda then this will happen automatically).</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Requirements</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">The follow non-python requirements must be installed:</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p"> -</span> libcurl (and the <span class="sb" style="color: #d14;">`curl-config`</span> config)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p"> -</span> zlib</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown">The headers and libraries for these are required.</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Usage</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown">Basic usage is as follows:</span>
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<li id="ae58b3ba4c54b6fadb279decb1690b71b8be4857">
<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#ae58b3ba4c54b6fadb279decb1690b71b8be4857"><strong>pyBigWig.c</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">@@ -197,7 +197,8 @@ char *getNumpyStr(PyArrayObject *obj, Py_ssize_t i) {</td>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//Return 1 if there are any entries at all</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hasEntries</span><span class="p">(</span><span class="n" style="color: #333;">bigWigFile_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bw</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bw</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nBasesCovered</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bw</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indexOffset</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// No index, no entries pyBigWig issue #111</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(bw->hdr->nBasesCovered > 0) return 1; // Sometimes headers are broken</span></span>
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<pre style="margin: 0;"> <span id="LC202" 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>
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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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="378" 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="379" 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">@@ -378,9 +379,10 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw</td>
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378
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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379
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</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 class="n" style="color: #333;">tid</span><span class="p">;</span></span>
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380
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">startl</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;">endl</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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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</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;">kwd_list</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"type"</span><span class="p">,</span> <span class="s" style="color: #d14;">"nBins"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exact"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</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="k" style="font-weight: 600;">static</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;">kwd_list</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"type"</span><span class="p">,</span> <span class="s" style="color: #d14;">"nBins"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exact"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"numpy"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">};</span></span>
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382
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="c"> <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;">chrom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"mean"</span><span class="p">;</span></span>
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383
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Py_False</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">starto</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">endo</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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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="c"> <span class="n" style="color: #333;">PyObject</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputNumpy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Py_False</span><span class="p">;</span></span>
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384
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">nBins</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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385
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="c"> <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//In the off-chance that something elsewhere got an error and didn't clear it...</span></span>
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386
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="c"></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">@@ -399,7 +401,7 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw</td>
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399
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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400
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"> <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>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="c"> <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;">PyArg_ParseTupleAndKeywords</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">kwds</span><span class="p">,</span> <span class="s" style="color: #d14;">"s|OOsiO"</span><span class="p">,</span> <span class="n" style="color: #333;">kwd_list</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">starto</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endo</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nBins</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exact</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="c"> <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;">PyArg_ParseTupleAndKeywords</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">kwds</span><span class="p">,</span> <span class="s" style="color: #d14;">"s|OOsiO<span class="idiff left">O</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">kwd_list</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">starto</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endo</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nBins</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exact</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="n" style="color: #333;"><span class="idiff right">outputNumpy</span></span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> <span class="n" style="color: #333;">PyErr_SetString</span><span class="p">(</span><span class="n" style="color: #333;">PyExc_RuntimeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"You must supply at least a chromosome!"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="c"> <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">@@ -464,11 +466,26 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//Return a list of None if there are no entries at all</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c"> <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;">hasEntries</span><span class="p">(</span><span class="n" style="color: #333;">bw</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyList_New</span><span class="p">(</span><span class="n" style="color: #333;">nBins</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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;">nBins</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="LC469" class="line" lang="c"> <span class="n" style="color: #333;">Py_INCREF</span><span class="p">(</span><span class="n" style="color: #333;">Py_None</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="c"> <span class="n" style="color: #333;">PyList_SetItem</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">Py_None</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITHNUMPY</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">outputNumpy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Py_True</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="c"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</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;">double</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nBins</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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;">nBins</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="LC473" class="line" lang="c"> <span class="n" style="color: #333;">val</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;">NPY_NAN</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"> <span class="n" style="color: #333;">npy_intp</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nBins</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyArray_SimpleNewFromData</span><span class="p">(</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;">len</span><span class="p">,</span> <span class="n" style="color: #333;">NPY_FLOAT64</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//This will break if numpy ever stops using malloc!</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">PyArray_ENABLEFLAGS</span><span class="p">((</span><span class="n" style="color: #333;">PyArrayObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">NPY_ARRAY_OWNDATA</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC479" 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="LC480" 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="LC481" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyList_New</span><span class="p">(</span><span class="n" style="color: #333;">nBins</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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;">nBins</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="LC483" class="line" lang="c"> <span class="n" style="color: #333;">Py_INCREF</span><span class="p">(</span><span class="n" style="color: #333;">Py_None</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="c"> <span class="n" style="color: #333;">PyList_SetItem</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">Py_None</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITHNUMPY</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC488" 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="LC489" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="c"></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">@@ -484,17 +501,27 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw</td>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyList_New</span><span class="p">(</span><span class="n" style="color: #333;">nBins</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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;">nBins</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="LC489" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">Py_INCREF</span><span class="p">(</span><span class="n" style="color: #333;">Py_None</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;">PyList_SetItem</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">Py_None</span><span class="p">);</span></span>
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492
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<pre style="margin: 0;">-<span id="LC492" 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="LC493" class="line" lang="c"> <span class="n" style="color: #333;">PyList_SetItem</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">PyFloat_FromDouble</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITHNUMPY</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">outputNumpy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Py_True</span><span class="p">)</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="c"> <span class="n" style="color: #333;">npy_intp</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nBins</span><span class="p">;</span></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;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyArray_SimpleNewFromData</span><span class="p">(</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;">len</span><span class="p">,</span> <span class="n" style="color: #333;">NPY_FLOAT64</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">val</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="c1" style="color: #998; font-style: italic;">//This will break if numpy ever stops using malloc!</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"> <span class="n" style="color: #333;">PyArray_ENABLEFLAGS</span><span class="p">((</span><span class="n" style="color: #333;">PyArrayObject</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">NPY_ARRAY_OWNDATA</span><span class="p">);</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" 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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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyList_New</span><span class="p">(</span><span class="n" style="color: #333;">nBins</span><span class="p">);</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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;">nBins</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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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</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;">Py_INCREF</span><span class="p">(</span><span class="n" style="color: #333;">Py_None</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;">PyList_SetItem</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">Py_None</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 class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></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;">PyList_SetItem</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">PyFloat_FromDouble</span><span class="p">(</span><span class="n" style="color: #333;">val</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="LC519" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITHNUMPY</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">val</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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<pre style="margin: 0;">+<span id="LC524" 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="LC525" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#a53acb6d60ac6a063886d0a7a1dd8f7184e6f980"><strong>pyBigWig.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">@@ -2,7 +2,7 @@</td>
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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 <structmember.h></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 "bigWig.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"></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;">#define pyBigWigVersion "0.3.1<span class="idiff left right">7</span>"</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;">#define pyBigWigVersion "0.3.1<span class="idiff left right">8</span>"</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC7" 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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"> <span class="n" style="color: #333;">PyObject_HEAD</span></span>
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<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#f5d848e7beeea87ec3202f19ebf1bce809c843bd"><strong>pyBigWigTest/test.py</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">@@ -308,3 +308,23 @@ class TestNumpy():</td>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">bw</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"/tmp/delete.bw"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">testNumpyValues</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pyBigWig</span><span class="p">.</span><span class="n" style="color: #333;">numpy</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="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://raw.githubusercontent.com/dpryan79/pyBigWig/master/pyBigWigTest/test.bw"</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">bw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyBigWig</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">bw</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">bw</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</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;">float32</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">equal_nan</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">bw</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"mean"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">bw</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"mean"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</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;">float64</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">equal_nan</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pybigwig/-/commit/a6dedc88e646bdc5745ed4d560484a718877ab5e#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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">@@ -62,7 +62,7 @@ module1 = Extension('pyBigWig',</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">include_dirs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'pyBigWig'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.3.1<span class="idiff left right">7</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.3.1<span class="idiff left right">8</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'A package for accessing bigWig files using libBigWig'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Devon P. Ryan"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ryan@ie-freiburg.mpg.de"</span><span class="p">,</span></span>
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